In order to reduce the initial disturbance of a missile which leave the rail sequence, based on Lagrange equation, Hertz contact theory and virtual prototyping technology, a dynamic model of a missile system which leave the rail sequence is established. Considering the factors such as clearance, thrust misalignment angle, thrust misalignment distance, mass eccentricity, initial acceleration impact, position and size of positioning block, the parametric design of the dynamic model and the numerical analysis of the influence of the missile's attitude are carried out. The results show that the initial disturbance can be effectively reduced by controlling the above factors within a reasonable range, the clearance should be controlled between 0.4~0.6mm, 0.4~0.8mm; the smaller the thrust eccentricity of the engine and mass eccentricity of the missile, the better; the initial acceleration impact has less disturbance to the attitude of the missile; the position and size of positioning block has influence on the attitude angle of the missile.