Because the gradient tolerate of the traditional proton magnetometer on the low side, so that cannot be guaranteed accuracy of magnetic survey in the region of geomagnetic field is inhomogeneous to resolve this difficulty, this paper deeply research the feasibility of enhancing gradient tolerate of the proton magnetometer by improved method of measure signal cycle.And filtrate powerful functions 32 bit embedded ARM IC as main control unit, developed new type high precision proton magnetometer.Through comparison test with CZM-5 proton magnetometer, prove the index of gradient tolerate of the new type high precision proton magnetometer not lower than 8 000 nT/m, satisfy design requirements of the project assignment book.Conclusion is that improved method of measure signal cycle can notably enhance gradient tolerate of the traditional proton magnetometer that is important technology index.