The invention relates to a control system and method for a long-term low-power biased loop operation of a multi-loop reactor. The control method comprises a downlink power control method and an uplink power control method. A biased loop operation control system is established, and a scientific and feasible control method is adopted, so that the stable operation and steady output problems of the unit positioned in a low-power state for a long time can be solved when a nuclear powered vessel performs self-propelled marine operation, reactor trip is not needed when the nuclear powered vessel operates at low power for a long time, namely the stable operation and steady output of the unit can be realized, and obvious economic benefits are achieved. The long-term low-power marine operation of the ship is realized, and the application range of the reactor is widened. Moreover, since the reactor trip is not needed in the power switching process, the low-power operation risk is reduced, and the safety and economic efficiency of the unit are greatly improved.