No one has control over his thoughts, and neither did Gautama. However, there are two important differences here:

Buddha had no self-referential thought, that is “Who am I?”, “What do I want?”, “Why am I unhappy?”, “Should I…?”, “I shouldn’t have…”, “I’d like to be more…”, “I need to develop…” etc. So in this sense, he had the ultimate control over his self-referential thought, because he ceased them all.

He could easily enter a place of no thought altogether, at will, and probably spent a lot of time at this place effortlessly even throughout his daily activities. Thought is only needed when one is doing something new, or is thinking about doing something new. If you just want to rest your body or doing something old and familiar, like walking, thought is not needed.