The purpose of developing the automatic evaluation system of C language program is to make computers replace teachers, so that students can learn domain knowledge independently. In this way, teachers can be liberated from tedious work, and students can learn domain knowledge freely. In this paper, an automatic evaluation system of C language program based on fuzzy clustering algorithm is established. This system is developed with B/S three-tier architecture, that is, the whole business application is divided into three layers: presentation layer, business logic layer and data access layer. Based on the above basic knowledge, this paper describes the analysis of learning behavior by FCM( Fuzzy c-means). According to FCM, the membership matrix and clustering center matrix are calculated, and finally the clustering results of learners with different learning enthusiasm levels are obtained. The research results show that the accuracy rate of the method used in this paper is 91.0582%. It can not only avoid giving full marks to opportunistic students, but also give a more reasonable score to students who don't have result files and output results. The score given is objective and accurate, which meets our actual needs.