In order to study the tolerance in missile vertical launching system (VLS), we simplified the assembly model and reconstructed it with mathematical methods, established the tolerance parameter and deviation angle mathematical formulas. Considering the assembly errors of guide rail in missile vertical launcher system, the effect of assembly gap parameters on the system was studied at first, and then dynamic simulation model was established, the relationship between assembly gap parameters and missile launching accuracy was researched. At last, the above relationship model and conclusions were used; a prototype simulation system was developed, providing foundation and guidance for design of missile vertical launching system.