Aiming at the increasing demand for fine and efficient detection of underwater magnetic field in the field of marine exploration, especially in the military field, a modular data acquisition scheme integrating magnetic sensors and underwater positioning sensors is proposed, and an underwater multi-parameter data acquisition system based on NI CompactRIO is constructed. The system integrates two cesium optically pumped magnetometers, fluxgate magnetometers, and underwater integrated navigation and positioning modules to meet the experimental requirements under different conditions. In order to solve the problem of data synchronization when multiple sensors are collected at the same time, a synchronization scheme based on the external Oven Controlled Crystal Oscillator reference signal source is proposed. While ensuring data synchronization in the underwater environment where PPS signals cannot be received, the influence of ambient temperature changes on synchronization is further reduced. The output signal measurement module of dual-channel cesium optically pumped magnetometer is realized by using the improved direct frequency measurement method. This method improves the frequency measurement accuracy on the basis of ensuring multi-channel consistency. The acquisition system is based on the modular design concept, which can efficiently complete the acquisition task, and is easy to integrate and has high application value.