Every author is happy to know you've read their book/books. Tell them which book/books you read. Pick out parts you liked and tell them what they are, and why you liked them. Ask them questions about why they wrote the book, or about any part you don't understand. Ask if more books are coming. Ask where their inspiration came from. Look up the author online and learn a little about him/her and tell them about connections to your own life from characters in their book, or from their lives.
Make your letter a conversation with them. Like you were interviewing, or had a chance to have lunch with them. What would you say?
Well, if you don't know what talk to him about, maybe you really shouldn't be writing the letter, but if you feel so compelled to do so, just tell him how you appreciate his work, and maybe how it's affected your life.