In order to understand the influence of the side plate structure on the flow field effect of the octagonal prism artificial reef, this paper is based on the computational fluid dynamics method (CFD), using large eddy simulation (LES) to analyze the octagonal prism type of four different side plate structures. The changes of the flow field around the artificial reef are numerically simulated. And the flow field effect indicators are analyzed with the volume of upwelling, the volume of wake vortex and upward transport flux. At the same time, the numerical model was verified by the water tank experiment. The results show that the maximum root-mean-square error between the experimental flow velocity of the flume and the numerical simulation flow velocity of the two sizes does not exceed 0.065. At 0° vertical upstream, the upwelling volume of type A, type C and type D reef is 35.6%, 244.1% and 80.1% higher than that of type B reef, and the volume of wake vortex is 193.5%, 115.8% and 88.8% higher than that of type B reef, respectively. The upward transport flux of type C and type D is greater than that of type A, and the maximum upward transportation flux of type C is 1.29 times that of type D. At different upstream angles, the correlation between the projected area of upstream surface and the volume of upwelling of types C and D is obvious，and that between the projected area of upstream surface and the volume of wake vortex of types C and D was small. The research results indicate that: the numerical simulation used in this paper is accurate and reliable. The increase in the number of side plates has a significant effect on improving the flow field effect of the octagonal prism artificial reef, especially the upwelling effect. When the lower side plate is fixed, the inclined side plate of the upper layer is helpful to enhance the upwelling effect of the reef, and the vertical side plate of the upper layer is helpful to enhance the wake vortex effect of the reef, and different side plate combinations will cause different flow field effects. The research results can provide a reference for the optimal design of reef cell and the setting of relevant retarding parameters in large-scale marine numerical models.