Applied a subdivision modifier and imported in Substance Painter 2, the result is horrible I made this model in Blender. This is the low poly model:


And this is high poly. I added a subdivision modifier and applied it. You can see that the UV map actually updated as well:



And this is when I imported it in Substance Painter 2. I exported model as .FBX:


As you can see, the bottom part is horrible. I just want to render it clearly, but you can see that some kind of zig-zag lines in the model.

I adjusted the tolerance and hardness parameters but it doesn't seem to work.

How do I get a clean result when exporting the high-poly version where the subdivision surface modifier has been applied?
You should get all the faces that are meant to be flat together as one face. The bottom face on the cylinder in your case should look like a flat face, but because it's made out of a lot of faces, it doesn't. 
Select one of the bottom faces:
 

press Ctrl+Shift+Alt+F to select all the faces that are on a 0 degree angle of it:
 
Now hit X and choose 'Dissolve faces'. Now you have erased the unnecessary vertices: