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To adapt themselves to the aquatic environment, fish have developed extraordinary propulsion and manoeuvring abilities. The physical and biological mechanisms observed in swimming fish can be applied to improve designs of Autonomous Underwater Vehicles (AUV), which can be used for the exploration of undersea resources. Fish swimming is a typical fluid-structure interaction problem, which involves several complicated mechanisms including vortex generation, the coupling of hydrodynamics and body-dynamics, as well as the interplay of fish body locomotion and the kinematics of multiple fins with flexural properties. Although relevant research has been carried out for several decades, there are still lots of phenomena behind aquatic swimming which are worth investigation. This work aims to improve the understanding of the underlying physics and sophisticated interactions in fish swimming. For this purpose, a coupled fluid-structure analysis tool is developed in the current thesis for solving aquatic biomimetic problems. The developed numerical tool takes advantage of the commercial CFD software ANSYS Fluent to solve the fluid field surrounding swimming fish with high fidelity and utilises the theory of Multi-Body Dynamics (MBD) to simulate the complex locomotion of various types of fish swimming, such as the undulating motion of fish body, self-propelled motion of fish with flexible fins. The MBD theory is implemented in ANSYS Fluent as User Defined Function (UDF). The coupling of these two solvers is achieved by compiling and exchanging force and motion data between the UDF and ANSYS Fluent at each time step. Additionally, to tackle the complex mesh movement in fish swimming simulations, a dynamic mesh function is employed to regenerate and smooth deformed computational mesh. A series of test cases is firstly studied to validate the various features of the tool, including three actuated connection cases (a discrete undulating fish, the undulating motion of a continuous Anguilliform fish, and the cupping motion of a fish peduncle- Abstract III caudal model) and one passive connection case (a flapping wing with two foils). Results obtained from all these cases meet well with previously published data, which successfully validate the coupled tool developed in this work. Subsequently, the study of a pufferfish model driven by its multiple fins is carried out to investigate the effects of rigid and flexible fins. Dorsal, anal and caudal fins are included in the model. The morphology and kinematics of the flexible fins are obtained from a live fish experiment. The deformation of the caudal peduncle and the spanwise deformation of fins are ignored. Hydrodynamic performance of the fish with rigid and flexible fins are investigated, focusing on their differences in induced velocity, hydrodynamic force, surface pressure, vortex structure, power and efficiency. The role of dorsal and anal fins during unsteady swimming is lastly analysed. Comparisons are made by simulating the pufferfish model with and without the dorsal and anal fins. A perturbation is given in the flow as a constant incoming velocity to study the performance of the models under unsteady flow conditions. The results are analysed from the following aspects: displacement, velocity, hydrodynamic force, power and efficiency. Interactions between the fish and fluid flow are analysed by visualising the vortices generated by the fish body as well as its multiple fins.