A towed Overhauser marine geomagnetic magnetometer used for weak magnetic anomaly detection in severe ocean conditions is studied to investigate means to reduce the negative effect of dynamic behavior and magnetic noise associated with ocean waves. For the dynamic effect, a continuous polarization workflow is proposed to enhance the free-induction-decay signal, and then, a multi-angle pickup coil and a self-tracking programmable amplifier are used to further reduce the adverse effect caused by uncontrollable changes in the towfish attitude on the signal quality. Furthermore, to achieve adaptive suppression of magnetic noise in different ocean conditions and areas, a modified adaptive Kalman algorithm is assessed. In addition, an optimized Overhauser sensor and a towfish were developed. Overall, the experimental results show that the sensor can effectively suppress the dynamic effect and magnetic noise. Regarding the magnetic sensitivity, uncertainty and range are 12 pT/Hz1/2@1Hz and 0.21 nT and 20 000 nT–100 000 nT, respectively. Moreover, underwater testing was performed to verify the function and the detection of the magnetic anomaly.