You could make it similar to a stone colossus where people can go inside it. You can give it an ability that allows for a much, much larger space to exist while inside the creature that's city sized.
As for what CR it should be or what else it should have I don't know.
How powerful do you want it to be? Because the only things in pathfinder close to this in size are the Cetus (1200 ft long fish) the zygomind (500 ft mushroom alien thing) and the Olphaunt of Jandelee which is said to be thousands of feet tall and they're Cr13, 18 and 30 respectively so you have room to manouvers with the strength you want it.
How powerful do you want it to be? Because the only things in pathfinder close to this in size are the Cetus (1200 ft long fish) the zygomind (500 ft mushroom alien thing) and the Olphaunt of Jandelee which is said to be thousands of feet tall and they're Cr13, 18 and 30 respectively so you have room to manouvers with the strength you want it.
Cetus is a dragon, lol. As for other big dudes, don't forget this guy
http://www.archivesofnethys.com/MonsterDisplay.aspx?ItemName=Aspidochelone
http://lostcityofatlanta.blogspot.com/2010/10/aspidochelone.html?m=1 (picture of it)
The DragonMech campaign setting (for 3rd edition D&D) had some rules for city-sized constructs.
However, I would probably just treat it as an castle or other large building (albeit one that happens to move like a vehicle). For example, its walls would have hit point scores like a castle, but could only be destroyed in small sections. It simply isn't the kind of thing players (even high level ones) should be able to destroy as a whole with swords and spells.
That little box above his profile says he's a dragon, but he is very clearly the proverbial bigger fish >.>
Wouldn't it be simpler to shrink the Dwarves?
What you're describing is bigger than size Colossal.
I would make what you're describing a hazard or environmental feature, rather than a monster.
Perhaps you should design a series of encounters, each one a different independent construct. To destroy the overall construct, you have to defeat all of the separate components in a specific sequence. You could then stat up those discrete encounters as separate monsters.
Bonus points if you set them up that each one defeated imposes some kind of penalty or otherwise reduces the effectiveness of the rest. That way, the PCs can figure out which ones to move against first.
So how would one go about stating a construct big enough to fit a city of dwarves in it's belly or should i just avoid giving it stats entirely and instead make it an environmental hazard, like a typhoon?
When you need a gaming map the size of a real city block to represent the monster in your encounter, the latter option becomes a lot more attractive.
You are blurring the line between an environmental hazard and an actual environment. I think that you might have better luck starting from ship movement/combat/whatever and going from there.
What are you trying to do with it, exactly. If it has to be a monster that you're planning on having it fight, too, I'd go with my first suggestion: making a colossal creature with a much larger than usual space. You don't have to have a city sized square space, as most creatures sizes are abstracted. Then have an ability that allows it to store 100,000+ medium sized creatures that are able to treat the inside of the creature as if it were an actual city. Honestly I'm not too much of a fan of janky concepts like dividing sections of creatures into separate pools of HP for a monster. Even vehicles don't work like that.
If it's not intended to fight or really have anything to do with combat, I wouldn't even make the thing on paper and just say it exists.