Cormorants (Phalacrocoracidae) are flipper-propelled aquatic divers which can achieve excellent takeoff capability from water surface. Computational fluid dynamics (CFD) collaborating with fluid-structure interaction has shown powerful capability for solving a variety of biomechanics problems of swimming locomotion. We implemented a flexible structural biomechanical 3-D flipper demonstrating the undulatory kinematics, in order to biomimetically synthesize realistic swimming mode. The skeletal kinematics of the flipper were constructed from the underwater swimming videos, and the soft flexible muscles were generated by the skeletal skinning algorithm. During the rapid take-off process, the cormorant used the flippers to beat the water surface at a high frequency to generate an oblique upward fluid reaction force, which cooperated with the flapping of the wings to generate lift and thrust. The cormorant’s posture adjustments during take-off, such as turning and pitching, require fine movements, which require small forces and moments to be generated by the wave of the flipper. The wave state of the flipper of a cormorant is similar to that of a fish caudal fin, which can produce some anti-Carmen vortex streets that are beneficial to the state of locomotion. Meanwhile, the asymmetric flipper locomotion could initiate turn maneuvers-evidence that cormorants may use their flippers to steer during swimming. These formulations and computational procedure also apply more generally to other fluid applications, such as underwater swimming or locomotion over water surfaces.