Rice improvement breeding is one of the most important research fields in China. With the development of modern rice breeding technology, hundreds to thousands of new varieties are produced daily, creating the impetus for rapid plant phenotyping evaluation. However, traditional measurement is inefficiency, contact-interferential, and lack-objectivity. Thus a high-throughput and automatic extraction system for rice plant is imperative. In this article we developed a rice phenotyping automatic extraction system and designed the automatic control for the system based on programmable logic controller (PLC). Subsequently, the prototype was test under industrial conditions continuous 24 h workdays and the error probability was less than 0.01%. In sum, base on PLC, we provide an efficient and stable automatic control system for pot-grown rice phenotyping inspection.