The water flow patterns around hollow trapezoidal reef and hollow square reef in unsteady flow effect were investigated based on CFD numerical simulation, the scale and intensity of upwelling and wake vortex region were revealed, and the flow field differences of monomer reef and combination reef were analyzed. The numerical results show that for trapezoidal reef,the maximum and average velocities of upwelling were about 0.58 to 0.67 and 0.15 to 0.19 times of incoming velocity, the maximum height of upwelling was about 2.12 to 2.49 times of reef height, the average velocities of wake vortex region was about 0.35 to 0.36 times of incoming velocity, the width of wake vortex region was about 1.40 to 1.61 times of reef width, and the length of wake vortex region was about 4.06 to 4.17 times of reef height. For square reef, the maximum and average velocities of upwelling were about 0.56 to 0.61 and 0.15 to 0.17 times of incoming velocity, the maximum height of upwelling was about 2.22 to 2.63 times of reef height, the average velocities of wake vortex region was about 0.30 to 0.35 times of incoming velocity, the width of wake vortex region was about 1.75 to 2.00 times of reef width, and the length of wake vortex region is about 3.90 to 4.06 times of reef height. From the point of flow field control effect, under the same simulation conditions, the square reef could perform better environmental and resources repair functions than trapezoidal reef.