Variation reduction in multistage assembly processes is an important but challenging issue for quality control. It is desirable to minimize the final product variance from a system level. Fruitful research has been conducted on this issue based on the fixed assembly order. However, the variability of parts can be affected by different assembly order. In this paper, we propose a quality control strategy that takes into account the assembly order in two stage assembly processes. Specifically, we analyzed the relationship between the final product variation targets and the assembly order. A case study in conducted on a two stage assembly process of vessel diaphragm to illustrate the developed methodology.disastrous.