Generally, model validation is mainly based on statistical analysis. However, when the sample size of real system output is small, it is difficult to obtain accurate validation results with classical statistics theory. In such a situation, a model validation method based on improved Bootstrap approach and Bayes estimation is provided. First, Bootstrap method is used to enlarge observed samples size and obtain Bayes prior distribution information. Then, Bayes theory which combines prior information and small sample data is used to estimate the statistical characteristics of observed samples. Finally, single-sample hypothesis testing is used to evaluate the credibility of simulation model. Furthermore, an improved Bootstrap method is proposed, which raises the accuracy of parameter estimation and extends bootstrap samples range beyond the original data. The numerical experiment results reveal the effectiveness of validation method and improved Bootstrap method.