The outlet pressure box culvert is often used as the drainage building of a pumping station. Because of its compact structure, it produces transverse flow velocity and then forms poor flow patterns, such as bias flow, reflux, and flow separation, which affect the discharge efficiency of the pumping station. Based on the combination of a physical model test and numerical simulation, the hydraulic characteristics of an eccentric tapering outlet pressure box culvert were analyzed. Focusing on the poor flow pattern in the box culvert, different optimization schemes were proposed to adjust the flow pattern. The flow pattern, transverse velocity distribution ratio (which represents the proportion of transverse velocity in velocity), average angle of the axial velocity, axial velocity uniformity, and pressure distribution of each scheme were compared to obtain the best scheme. The results show that the combination scheme of “diversion pier position and angle with deflecting flow baseplate” has the best optimization effect on the flow pattern. This scheme can effectively improve the bad flow pattern, significantly reduce the transverse velocity distribution ratio, and make the pressure distribution on both sides of the long diversion pier uniform. The axial velocity uniformity was increased by 17.45%, and the average angle of the axial velocity was increased by 8.23°.