Aiming to the interference problem of random factors, the effect of motor thrust misalignment on launching precision is studied. A rigid-flexible coupling model of vehicle-mounted missile vertical launch is built with the virtual prototype technology and modified Craig-Bampton method. To get the sample data of missile attitudes in different working conditions, the thrust misalignment angle parameterized dynamic simulation based on Monte Carlo method is used. The data statistical analysis based on histogram and maximum likelihood estimation is used to analyze the distributions of related missile attitudes, and the relationship between thrust misalignment and initial disturbance is established. The research results show that the distributions of related missile attitudes are approximate to normal distributions considering the influence of thrust misalignment.