Pufferfish swim and maneuver with a multi-fin system including dorsal, anal, caudal, and pectoral fins, which presents sophisticated ventures in biomimetic designs of underwater vehicles. Distinguished from those ‘typical’ fish with streamlined body shape and body-caudal fin (BCF) undulations, pufferfish adopt non-streamlined plump body shape and rely on the oscillations and interplay of fins to achieve high performance maneuvering. Aiming at unveiling novel mechanisms associated with multi-fin kinematics and hydrodynamic performance in pufferfish swimming, we carried out an integrated study by combining measurement and digitizing of multi-fin kinematics and three-dimensional deformations and computational fluid dynamic (CFD) modeling of steady swimming. We constructed a realistic multi-fin kinematic model to mimic motions and deformations of the dorsal, anal, and caudal fins. We further built up a CFD model of the pufferfish with a realistic body and multi-fin geometry to evaluate the hydrodynamic performance of its multi-fin system. Our results demonstrate that in pufferfish steady swimming, caudal, dorsal and anal fin rays oscillate while performing significantly passive bending and twist deformations but show a noticeable out-of-phase feature, leading to neutralizing rotational forces and hence suppressing yaw motion, particularly at fast swimming. Numerical simulation suggests that the caudal median fin plays a key role in thrust generation while the dorsal and anal fins also provide a considerable contribution.