How to give opinion to my professor about writing LoR? I have been applying to PhD positions (got offers already, thanks god) and surely I asked my master thesis supervisor as one of my letter writers. 

He is quite new as a PI. He told me that it is his first time to write a recommendation letter for PhD applications.

I had a really good time working with him and believe that he is nice and thinks good of me. (of course, he may secretly think that I am stupid).

The problem is that I actually received a feedback from a position that rejected me suggesting that my reference is not very strong. On top of that, (maybe just by coincidence), I didn’t include his letter in my successful applications.

As he is lack of experience, I doubt that his way of writing the letter may be too subtle or not giving enough details or such. (Again, of course, he may secretly think that I am stupid.)

As it will possibly be good for him and any of his later students, should I hint him about this? If yes, how should I say it nicely?

Thank you.
I have two suggestions. The first is to give him an outline of what you think your accomplishments are and say something about your enthusiasm and future goals. Or, at least, offer to give him such an outline if it would help. This is just to give them a few ideas. 

The second, probably more important, is that you ask another, more experienced, professor that is also writing for you, to speak with the advisor and also give them ideas about how to frame such a letter. It is normal for one professor to help out another, newer colleague, on their responsibilities. 

I'll note that some letter writers actually ask the candidate for a first draft of the letter they will send. There is some controversy about this, but it is common enough that you shouldn't be surprised if it happens.