Part of Page breaks After convert to theme

Hi people, I am having a very strange problem here.

I’ve created a theme from scratch. I converted it to wordpress theme, and it is broken.

Strange thing is I copied the whole Page Source of the broken theme from the browser (View Source) and paste it into a textfile and save as a normal html. It worked.

Now come the frustrating part, from that html file (now clean from ALL traces of php codes since it is from View Source), I saved it as the index.php of my custom theme, guess what, the layout collapsed again! Even without a single line of php code, it collapsed, just because it is a .php file called by wordpress engine to become a theme. It looked completely fine when it is still a .html

So I suspect something is wrong when wordpress calls my theme file. It messed up my css structure in between the process. But I donno how to fix it…

Anyone got any idea?