Marine sediment transport is closely related to seafloor topography, material transport, marine engineering safety, etc. With a developed time-series vector observation device, the sediment capture and transport process can be observed. The structure of the capture tube and the internal filter screen can significantly affect the flow field during the actual observation, further influencing the sediment transport observation and particle capture process. This paper presents a numerical model for investigating the effect of device structure on seawater flow to study the processes of marine sediment transport observation and sediment particle capture. The model is based on the solution of both porous media and the Realizable k-ε turbulence in Fluent software. The flow velocity distribution inside and outside the capture tube with different screen pore sizes (0.300, 0.150, and 0.075 mm) is analyzed. To enhance the reliability of the numerical simulation, the simulation calculation results are compared with the test results and have good coincidence. Finally, by analyzing the motion law of sediment in the capture tube, the accurate capture of sediment particles is achieved, and the optimal capture efficiency of the sediment trap is obtained.