The invasions of marine organisms into the intake of nuclear power plants threaten the normal operation of such plants. Most published numerical models assumed that marine organisms passively follow the current, but such models neglected their biological swimming ability. In this work, adopting a hydrodynamic mathematical model to replicate the flow around the Daya Bay nuclear power base, the invasion characteristics of Acetes were explored by considering the behavior of biological movement. A concept of biological residual current was introduced to describe biological movements that were dominated by both tidal current and biological swimming ability. The biological residual currents near the nuclear power plant were obtained for cases with different nocturnal migration periods (12 h, 13 h, 14 h, 15 h, and 16 h). Using the Lagrangian particle-tracking method, the primary invasion paths of Acetes were obtained, as well as the travel time of Acetes to the intake, based on the biological residual current along monitoring points. The results showed that the invading time for Acetes reaching the water intake of the nuclear power base was significantly decreased when biological migration behavior was considered. When the nocturnal active period was over 13 h, it took only 10 days for Acetes to enter the western waters of Daya Bay from the southwest of Da Lajia Island and then continue migrating to the water intake in the nuclear power base. When the nocturnal active period was less than 13 h, it took more than 20 days for Acetes to travel the same distance. The present work provides a new methodology for the simulation and prediction of the migration of marine organisms.