I am new to github pages so I made the following repo with a simple index.html https://github.com/jigneshjain25/jignesh.github.com/blob/gh-pages/index.html
but http://jignesh.github.com/ shows "Hello World" only. Why its not using my index.html file?
You're not publishing to the master branch, but the gh-pages branch, yet you are trying to deploy a user page. Also it needs to be http://jigneshjain25.github.com because that's your username.
https://help.github.com/articles/user-organization-and-project-pages
The account that controls that Hello World has been set-up properly, here:
https://github.com/jignesh/jignesh.github.com/blob/master/index.html