The utility model is suitable for a magnetic field measuring equipment technical field provides a proton magnetometer control system, and it is limited to aim at solving current system's operational speed and function, and its chip volume is bigger than normal, is unfavorable for the problem of the miniaturized design of instrument. This system cushions and incites somebody to action including being used for carrying out the logic input to received precession signal the unit is kept apart to the digit of precession signal conversion square signal and logical buffered output, a real -time clock unit for provide test time in real time, be used for receiving square signal to obtain through capturing module test time that two continuous rising edges of square signal correspond and the frequency of real -time clock unit calculates the DSP signal processing unit of precession frequency, test time does during two continuous rising edges the time value of the record of real -time clock unit, unit and real -time clock unit are kept apart to the digit output respectively with DSP signal processing unit's first input end, second input electric connection.