The low-frequency pulsation of the marine hydraulic system is transmitted along the pipe, which can create structural vibration. For the low-frequency pulsation which is difficult to control by passive style, a by-pass secondary source was designed and the pulsation control research by active style was carried out. The designed by-pass secondary source was driven by piezoelectric ceramics, which is compact and has an amplification structure to improve response characteristics. The active control system of the hydraulic system was built, and the FxLMS adaptive algorithm was used to control the pulsation at multi-frequencies. The experimental result shows that the by-pass secondary source can effectively attenuate the low-frequency pulsation at multi-frequencies, and can reduce the vibration energy transmitted with the fluid, which has no negative effect on the working performance of the original hydraulic system.