During the process of software development, activities of programmers including copy and paste result in a lot of code clones. However, the inconsistent code changes are always harmful to the programs. To solve this problem, and find harmful code clones in programs effectively, a method was proposed to predict harmful code clones by using Bayesian network. First, referring to correlation research on software defects prediction and clone evolution, two software metrics including static metrics and evolution metrics were proposed to characterize the features of clone codes. Then the prediction model was constructed by using core algorithm of Bayesian network. Finally, the probability of harmful code clones occurrence was predicted. Five different types of open-source software system containing 99 versions written in C languages were tested to evaluate the prediction model. The experimental results show that the proposed method can predict harmfulness for clones with better applicability and higher accuracy, and further reduce the threat of harmful code clones while improving software quality.