Rice is a key food of humankind, the third largest food crop in the world, behind only corn and wheat. The process of removing the rice husk, the rice skin portion, and the rice germ to make white rice is called rice milling. This empirical study applied some tools (Cause-and-Effect Diagram, QFD, FAA and TRIZ) to improve the quality of rice milling. At first, this study used Yixing Rice Milling Company in Taiwan to illustrate the process of fully automated rice milling. There are eight steps in the rice milling process system: testing, drying, refrigeration, hulling, milled rice, rice washing, color sorting, and packaging. Second, using risk assessment theory, the eight steps of the process were evaluated to determine which steps were the most vulnerable to risks. Four key factors in poor milling quality were identified: the hue recognition subsystem, the cold storage structure, ventilation, and the air pressure nozzle subsystem. Finally, the four key factors were improved with systematic innovation methods (TRIZ). We then made recommendations for improving the quality of rice production operations to Yixing Rice Milling Company.