The activities of the programmers including copy, paste and modify result in a lot of code clone in the software systems. However, the inconsistent change of code clone is the main reason that causes program error and increases maintenance costs in the evolutionary process of the software version. To solve this problem, a new research method was proposed. The mapping relationship between the clone groups was built at first. Then the theme of lineal cloning cluster was extracted using Latent Dirichlet Allocation (LDA) model. Finally, the inconsistent change probability of code clone was predicted. A software which contains eight versions was tested and an obvious discrimination was got. The experimental results show that the method can effectively predict the probability of inconsistent change and be used for evaluating quality and credibility of software.