But that's all through Chief Bromden's eyes. Remember that at the beginning of the book, Chief Bromden is bummed because he's so small. They did something to him to make him small, and at some point much later, he notices that he's big again, and wonders how McMurphy did that. At the end, he comments on how there's no way that's McMurphy. He's too small. Where are those huge arms? He's just not big enough. Why? Because the light has gone out in his eyes. McMurphy "in reality" may not be a very big man at all, but because he's loud and cocky, he seems larger than life. After the procedure, he's small.
Chief Bromden is a huge man, but originally thought McMurphy was much bigger than him. It's all perception. That's one of the points of the story.