Cormorants (Phalacrocoraxe), types of aquatic birds, utilize the compliance/flexibility of the flippers and exploit hydrodynamic/biomechanic processes to accomplish diverse operations. Particularly, the flipper‐propelled locomotion exhibits traits such as super‐redundancy and large deformations, necessitating depiction of both movements of the rigid skeletons as well as local deformations of the soft tissues. However, there are few well‐established kinematic/hydrodynamic framework models and constitutive equations for such rigid–flexible intrinsically coupled biosystems. Herein, combined with a skeletal skinning algorithm to handle the deformation of a flexible body attached to a rigid body, a numerical computation framework for an in‐depth fluid–structure interaction is presented, which enables the capture of viscoelastic and anisotropic characteristics of a highly compliant 3D rigid–flexible coupled model in a low‐Reynolds‐number flow. Considering the biorobotic cormorant flipper with a nonuniformly distributed stiffness as a representative, the challenging issue of controlling a biomechanically compliant flipper to synthesize realistic locomotion sequences, including rigid skeleton movements and soft tissue deformations, is addressed. Furthermore, a numerical computational hydrodynamic analysis is performed to demonstrate that the cormorant flipper can generate 5 N fluid force and 0.45 N m fluid moment during the turning operation in 0.8 s, which is consistent with the former experimental results.