The underwater pigging manifold system has the advantage of utilizing production fluid pigging and non-stop pigging, which has a broad application prospect in the current and future offshore oil and gas development. The structure of underwater pigging manifold is complex, there are many bends and reducing tees, and the production fluid pressure is high. However, the deformation and vibration of the underwater pigging manifold structure caused by the pigging technology is still unclear. The displacement, stress distribution and vibration of an underwater pigging manifold under fluid-structure coupling condition were calculated by numerical simulation. It is found that the valve switch is the characteristic moment with the largest range of pressure change, and also the characteristic moment that causes the most serious displacement and vibration of pipeline. It is clear that the risk site of pipeline structure is the end of manifold structure, the maximum displacement is about 5.69 mm, which is mainly contributed by the X direction, and the maximum equivalent stress is 233.13 MPa, which is mainly distributed at the inside of T-shaped pipe and bend pipe. The optimal support scheme was proposed. The maximum displacement of manifold structure is reduced to 3.53 mm, and the increase of low-order modal frequency is about 1.74% ~ 20.54%. The safety of manifold structure is improved. The research results can provide theoretical basis for the design and operation of underwater pigging manifold.