The square cap is a typical semi-submersible component of sea-crossing bridges, which connects piers and pile-group foundations. As the cap size is large, it usually has a non-negligible influence on the wave motion around the pile-group foundation, so it is not considered in the relevant specification. However, neglecting this influence may have adverse effects on the structure. In this paper, the wave forces on capped pile groups are simulated by a numerical wave flume. Firstly, the numerical flume used in this paper is validated by an experiment in the previous literature. Then, capped pile groups with different arrangements and different water levels are modeled to study the interference effect of the square cap on the wave force, and the variation law of the interference effect coefficient Kcp of the cap is given. Next, we introduce Kcp into the theoretical formula of wave forces on pile groups and obtain a modified formula that considers the cap effect. To verify the feasibility of the modified formula in practical engineering, we use the formula to calculate the wave forces acting on capped pile groups of a sea-crossing bridge. The results of the modified theoretical formula are compared with that of the numerical water flume and recommended values in the specification. It is found that the theoretical values are relatively close to the numerical results, while the specification values tend to be conservative. The modified theoretical formula proposed in this paper and the obtained parameter distribution law can provide a reference for engineering design.