The sewage often deposites in inverted siphon tunnel and even blocks the tunnel. Hence, a new type of intelligent sewage discharge structure for work shaft of inverted siphon tunnel is proposed. The tunnel and working shaft are modeled and numerically simulated by software SolidWorks, and the physical model test is carried out. The research results show that: (1) The addition of the auxiliary block helps to reduce the turbulent flow position; and changing the flow velocity of the inlet at a certain extent has little effect on the water diversion structure. (2) The scheme of adding a rectangular triangle block in the work shaft and the scheme of adding a stepped double triangle block in the inlet zone and the rectangular triangle block in the exit zone are the optimal intelligent sewage drainage schemes for the inverted siphon tunnel. (3) The size of the rainwater gully section will affect the turbulent flow position and velocity distribution of the water flow, but the appropriate auxiliary block would still achieve a better intelligent sewage discharge effect.