Abstract: The intake and drainage system of cooling water is a key component of coastal power plant projects. In recent years, as China’s nuclear power development has steadily expanded and shifted toward offshore islands, increasingly complex wave conditions in open sea areas have made wave forces a primary factor affecting the safety of drainage structures. The steel cap-type variable cross-section drainage riser structure is a commonly employed configuration in the drainage engineering of coastal power projects. In this study, a three-dimensional (3D) wave physical model test was conducted to simultaneously measure the inline force, transverse force, and uplift force acting on the steel cap-type variable cross-section drainage riser. The temporal variation of the forces on the variable cross-section drainage riser was analyzed, the effects of water discharge and submergence depth on the forces were examined, and calculation methods for the inline and transverse forces of the variable cross-section drainage riser were developed. The 3D wave physical model test was performed in the wave basin of Nanjing Hydraulic Research Institute, which has dimensions of 50.0 m in length, 17.5 m in width, and 1.2 m in depth. Wave-absorbing slopes or plates were installed around the basin to reduce wave reflection. The results of the 3D wave physical model test indicate that under the combined action of waves and water discharge, the forces on the drainage riser display periodic variations, with the force variation period corresponding to the wave period and accompanied by high-frequency fluctuations. These high-frequency fluctuations may be attributed to the turbulent state of the discharged water inside the pipe and the pulsating behavior of water particle motion. By comparing the peak values of the uplift force, inline force, and transverse force on the drainage riser structure, it is found that the uplift force is the largest, followed by the inline force, while the transverse force is slightly smaller than the inline force. The influence of the transverse force on the drainage riser structure cannot be ignored and must be highlighted in future engineering design. Regarding the timing of the peak values of the uplift force, inline force, and transverse force on the steel cap-type variable cross-section drainage riser structure, the peaks of the inline force and transverse force occur simultaneously, indicating no phase difference between them. However, the peak of the uplift force does not coincide with that of the inline force or transverse force, showing a phase difference of approximately π/2 between the uplift force and the inline or transverse forces. Water discharge has almost no effect on the phase relationship among the inline force, transverse force, and uplift force. Water discharge significantly amplifies the uplift force, with an increase ranging from 25% to 75%. The uplift force under the combined action of waves and water discharge exceeds the linear superposition of the force due to waves alone and the force due to water discharge alone. In contrast, water discharge has no significant amplifying effect on the inline force and transverse force of the drainage riser. The relative submergence depth is a key parameter affecting the forces on the drainage riser. The relative maximum inline force and transverse force occur at a relative submergence depth of zero, while the relative maximum uplift force occurs at a relative submergence depth of 0.013. For small-scale variable cross-section drainage riser structures, the Morison equation can be applied for segmented calculation. However, for the force calculation of the perforated structure, a void ratio reduction coefficient should be introduced. By incorporating this coefficient, the wave force on the perforated structure can be calculated with a maximum error of less than 4%. The wave force calculation method for variable cross-section perforated drainage riser structures proposed in this study can serve as a reference and validation for future similar engineering designs and numerical simulations.