How can I make the Custom Templates only for Mobile View.
example :
When my user open the site on computer then it should open on the default design
but when my user open the site on mobile then it should use the Custom Templates
That should be possible by using JavaScript, but why the default responsive page is not good in mobile mode? Are the 2 versions very different in your project?
You should keep using Custom Templates; either for Desktop or Mobile view/mode. However, you may simply create your own CSS class to hide the element in the Desktop and/or show the element in the Mobile; or vice versa, and use it in you Custom Templates.
Google "bootstrap css hide on desktop", there are so many useful resources out there that you can use in your Custom Templates.