I know my Question is little bit basic but have to ask about this:
i have my website build in Visual Studio 2008 with .Net framework 3.5 that site is hosted on my server.
now because of some specific reason i have to install framework 4.0 to the server. and i just want to know that my site will be okk with it or not.
I mean if i change my framework from 3.5 to 4.0 then is there some changes i should make to my site or that site will run fine as before.
You should also change Framework Version in the application pool of your WebSite.
Basically, remember that Framework version != CLR Version.
In your case, .NET Framework 3.5 = CLR 2.0 + (C# 3.0 | VB9)