How to ask for lettler of recommendation from supervisor when he would be interacting very little with me?
The solution seems fairly simple. At your next meeting with this professor, or one you can arrange sooner rather than later, let him know of your future plans and that you will eventually want to ask him for a letter. Make a special request that he "follow your work" enough that he can write such a letter. But also ask hime for advice about how to be a success in the project and to prepare yourself for later academic work. 

The goal is just to get him to notice you even if you aren't interacting much. But, of course, this assumes that your work will be very good overall so that there are only good things to say about you when the time comes. 

It is helpful for a professor to know that students have certain aspirations beyond the current project/course/degree. Make him aware early on, rather than later.