Java Programming, as a core course for computer professional programming courses, has the characteristics of much concept, abstract knowledge points and difficult understanding. Many students do not have real programming ideas after learning this course. Therefore, this article takes the students of college of computer science and technology in liupanshui normal university as the research object, comparing the common teaching mode and computational thinking and flipped classroom teaching mode. Research shows that the computational thinking and flipped classroom used in Java programming can help students understand the abstract knowledge, fully arouse the enthusiasm of students learning, improve the students' practical ability, and gradually cultivate students the ideas using algorithm to solve problems. It lays a solid foundation for the future programming work.