To offset the weakness of acoustic surveillance system, a underwater magnetic surveillance system was designed for port protection. A three classes' bus topology structure was adopted. The system comprised scene devices, transmission cable, and console. The scene devices included several gateways and more nodes with a magnetometers array. Three protocols of RS-485 bus, CAN bus, and CAN-Ethernet transform was designed for data transmitting. Nodes worked in autonomous intelligent mode based DSP microprocessor. Each node managed a magnetometers array via RS-485 bus, implemented signal sampling as well as target detecting and positioning, and sent results to the gateway via CAN bus when need. The principle prototype consisting of a console, a gateway, and three nodes with an array of ten magnetometer cells was developed. The experiment results prove the system effective.