Quality control (QC) plan is an important component of manufacturing planning for mass customization. QC planning is to determine the operational tolerances and the way to control process variation for assuring the production quality against design tolerances. It includes four phases, i.e., tolerance stack-up analysis, tolerance assignment, in-process inspection design, and the procedure of error source diagnosis & process control. Previous work has been done for tolerance stack-up modeling based on the datum-machining surface relationship graph (DMG), machining error analysis, and worst-case/statistical method. In this research, the tolerance stack-up analysis is expanded with a Monte-Carlo simulation for solving the tolerance stack-up problem within multi-setups. Based on the tolerance stack-up model and process capability analysis, a tolerance assignment method is developed to determine the operation tolerance specifications in each setup. Optimal result is achieved by using tolerance grade representation and generic algorithm. Then based on a process variation analysis, a platform is established to identify the necessity of in-process inspection and design/select the inspection methods in quality control planning. Finally a general procedure is developed to diagnose the error sources and control the process variation based on the measurements.