In recent years, photon frequency conversion technology has become a research hotspot that breaks through the key performance indicators of microwave signal frequency conversion. However, the inherent working state of photon frequency conversion is not stable, which makes the technology difficult to be applied. A photon frequency conversion control system for a single electro-optic external modulator is designed, which is specially used to realize the fast, accurate and micro disturbance regression after the best photon frequency conversion working point drifts. The system takes advantage of the comprehensive advantages of hardware and software, extracts the micro variable parameters of the photon frequency conversion working point by the calculus algorithm, and returns the drift working point to the best frequency conversion working point quickly and with micro disturbance by the proportion algorithm of control variables.