With the rapid development of aircraft industry, manufacturing department needs to put forward higher requirements for the accuracy of aircraft assembly. It not only affects the overall quality of the aircraft but it also affects the cost of aircraft manufacturing. This paper introduces the ways about the improvement of the assembly accuracy and guarantee of the quality of assembly, based on the conventional tolerance design, using 3DCS tolerance analysis software. It also elaborates on the tolerance design modeling technology and shows the simulation model of how tolerance analysis is set up. The VSA and 3DCS software are compared and the application methods that could be used in the design of aircraft assembly of the 3DCS tolerance simulation analysis software are discussed. The simulation of how the tolerance design is carried out for the assembly of aft fuselage and hatch door. The results are gained about the analysis of the assembly tolerance accordingly with the distribution, it directly analyses the aft hatch door dimensions under coordination of assembling. The necessary improvement and comprehensive optimization about dimensions ensure the quality and efficiency of the assembly of aft aircraft hatch door.