As the anti-rolling tank controller based on PLC is unable to fulfill the high strength of calculation of the automatic real-time control algorithm, which leads to the limitation of anti-rolling effect, this paper proposes a distributed embedded controller based on CAN bus communication. The controller uses a high-performance ARM chip as the main chip to meet the complex algorithm calculation requirements. For CAN bus communication between the distributed modules, the system is simple and reliable. Distributed embedded controller consists of the center controller, the IO controller and the communication adapter whose hardware design and software design are proposed in this paper, and achieves the acquisition of real-time data of ships status information and intelligent control algorithm. Through simulation and bench simulation experiments, the controller can achieves the excellent anti-rolling effect. The distributed controller architecture is simple and easy to expand and spread to various tonnages of real ships.