First off, the cover is pretty normal for The Mortal Instruments. Russell Gordon has a very distinctive style with the editing of these covers: the light illuminating from the runes, the city scape, the model(s) on the cover where you can't see their entire face (Though City of Fallen Angels was an exception to this with Clary's face on full view). This cover incorporates all of the classic details.
The first thing I noticed was that Clary was wearing white. In Shadowhunter culture, white is the colour of mourning - the sort of thing that would be worn to a funeral. Cassie has already told us that there will be a number of deaths in the book (6 characters that we already know, I believe is the number she gave us). Does this mean that someone close to her dies? Simon, Luke, Jocelyn... Possibly even Jace. Again. In today's society, white also represents purity and "good", so it could be saying something about, as Simon put it, "team good" and "team evil". She is also holding the hilt of a weapon. The way that she is holding it implies that instead of using it to slash at something, it was used to stab. Who did she stab? It could have been Sebastian, considering he's right in front of her. It could also be representing the Angel blade which Clary had used to stab Jace with (and causing his body to be filled with heavenly fire - which is what the book is named).
Next there is Clary's posture to consider. See how she's standing with her back towards the viewer? This could be representing her turning her back upon something or someone. The clave? Jace? But she also isn't facing Sebastian full on. She's turned slightly away, as though she's trying to avoid him but he's in the way. Or she's trying to avoid the disaster that would surely follow him. Though it's difficult to see, it looks like she's looking downwards. Possibly, she could be looking at the disaster that's around her on the cover.
Clary's hair is something in itself. Besides it slightly mimicking an old Windows screen saver, it also looks like fire (*cough* City of Heavenly Fire *cough*). This could be because she was the one who put the heavenly fire into Jace. Also, in City of Lost Souls, Sebastian says that "this world will be consumed by hellfire." Could some of the bad things that happen in the book be because of Clary herself - making her almost a personification of this "hellfire" that Sebastian speaks of?
Enough about Clary. Sebastian is standing in a shadow, looking at Clary. The juxtaposition between the light Clary and the darkened Sebastian could be representing the fact that Clary is more angel while Sebastian is more demon. It could also represent (along with the fact that Clary is facing the darkness) that the ginger may be joining Sebastian on the "dark side." It's a bit of a stretch, but hey. Anything could happen in this book. Sebastian's gaze in Clary's direction could be showing that he wants something that he cannot have. As shown in the book prior, there are some seemingly sexual feelings on his end towards his sister (going into incest there, click here to see Clare on the topic). It could also been seen as slightly hateful or resentful, considering Clary had put a damper on his plans by taking Jace away from him..
And then there are Sebastian's wings. The wings are a reoccurring thing throughout the books - mostly in Clary's dreams. I assume that it's safe to say that they are supposed to represent his demonic angelicness. If my memory proves correct, in one of Clary's dreams she had seen him with dark wings (though please do correct me if I'm wrong). I doubt that he will actually grow wings in the book. On the other side of this, the wings could be there to represent that fact that some angels may be appearing in this book. As Raphael put it in CoLS, "even the Angels will be destroyed." So will there be a mildly more friendly appearance of angels in this book? Or will they appear to scorch some Shadowhunters (or Sebastian's crowd). It could also be referencing to the ending of the previous book where Sebastian had placed a pair of bloodied angel wings in the New York Institute.
Then there is the background. This cover is the first one in the series in which the city scape is behind the character(s) on the cover. So why the sudden change? This could be because the world is coming to an end and that life as they [the characters] know it. This idea is also supported by the parched and cracked land in front of it. But back to the city for a moment, what city is it? It would be a bit of a stretch to say that some of the buildings look similar to the ones of the cover of City of Glass, considering most taller structures do look pretty similar when you can't see any small details on them. But there are a few pointed buildings which, in fact, imply that this may be Alicante. It's a possibility that this landscape is indeed the home to the Nephilim.
As for the fire in the foreground, part of that comes into the obvious bit that it comes from the title of the book. It's implied through the dry land right behind it that the fire consumed part of it. This could be literal and have fire sweeping across lands. Raphael in CoLS seems to have a pretty good prediction of things as well, proved when he said "there is a great darkness coming it will sweep the Earth with fire and shadow." There is certainly earth being shown, along with fire at the foreground and Sebastian as the shadow.
So what does the cover say about City of Heavenly Fire as a whole? Well, we can be sure that this book is going to be dark - most likely the darkest out of all of them - with a whole lot of feels to go around. The book will be released on on 27 May, so it's not too far now!