In order to improve the precision and anti-interference ability of traditional proton magnetometer, and provide reference basis for developing Overhauser magnetometer, a high precision proton magnetometer based on a multi-channel frequency measurement was designed. This paper introduces the basic principle of larmor precession effect, makes a detailed description about the signal disposal system and the multi-channel frequency measurement algorithm of the instrument. Finally, the comparison experiments between the proposed instrument and commercial Overhauser magnetometer under outdoor was conducted; the test results show that the performance of the instrument is close to that of the commercial Overhauser magnetometer; the proposed instrument has the advantages of convenient for field operation, high field magnetic measurement precision, strong anti-interference and etc, which proves the effectiveness of the proton magnetometer based on the multi-channel frequency measurement in weak magnetic measurement.