Fuel injector is the key part of a high-pressure common rail fuel injection system. Its manufacturing precision and assembly quality affect system's property and performance. According to the characteristics and demands of assembly of the fuel injector, an intelligent optimization algorithm is proposed to resolve the problem of assembly sequence planning. Based on geometric modeling, assembly dimension chain of the injector control chamber is established, and the relationship between assembly tolerance and volume change of control chamber is analyzed. The optimization model of the assembly is established. The impact of assembly tolerance on injector's performance is simulated according to the optimization algorithm. The simulation result shows that quantity of injection fuel changes correspondingly with the change of assembly tolerance, while injection rate and pressure do not change significantly, and the response rate of needle considerably slow. Similarly, the leakage rate of fuel in control chamber is calculated, indicating that the assembly tolerance has obvious impact on fuel leakage and its rate. The study illuminates that injector's assembly tolerance has prominent effect on injection.