For evaluate the risk of civil marine nuclear power plant, through the searching related standards for ship, external environmental parameters that the nuclear ship should be suited was found. Based on the characteristics of power plant of civil nuclear-powered ship, the hierarchy system of primary loop system was established and corresponding indicator marking criteria were formulated for the risk assessment. The result shows that the Reactor Safety Injection System (RIS), the Reactor Boron and the Water Supply System (REA), the Control Rods and the Hull of Fuel Canning are the key risk factors in the primary loop system. Finally, the comprehensive evaluation was carried out for collision, stranding and swing of multi-degree of freedom, and put forward relative countermeasures to cope with the possible risks based on the comprehensive evaluation and combined with the literatures.