The occurrence of aquatic organism aggregations near the inlet of nuclear power plant (NPP) has become an important issue around the globe, since the aggregated organisms can block the cooling system and threaten the operation safety of NPP. In this study we focus on the trajectory of aquatic organism, i.e., how these organism can be transported to the inlet of NPP by ocean physical processes related with currents and waves. The Changjiang NPP located at the west side of the Hainan Island in China experiences serious gulfweed blocking events occasionally in spring. In order to study the physical mechanism, with the use of a 3D numerical wave-current coupled model, the current and wave conditions near the NPP is simulated. Based on the model, several particle tracking simulations were run to evaluate the extent of the blocking occurred in the inlet of the NPP’s cooling system under different cases. Results show that the surface stokes drift induced by waves is the main cause for the blocking events in the Changjiang NPP, while the wind-induced shear current contributes a few as well. Further simulations revealed that bending of the inlet, changing offshore mouth to downstream mouth can prevent the blocking greatly, as the particle seldom transports into the mouth by the surface stokes drift. We suggest such findings may provide reference value for the prevention strategies of the aquatic organism aggregation events occurred in other NPPs.