Hello tuhinabid,
Thank you for your question about hacked site file issues. There are many different ways that the files of a site can be hacked. We have a few guides on hacks, including how to recover from a hack and what to do if you think your website has been hacked. Without knowing what kind of files and code you are using or whether or not you are using a content management system, I can best advise that you take a look at the articles listed and see if they can isolate from where your issue might be deriving.
Best,
Christopher M.