The box-girder superstructure of coastal bridges is vulnerable to wave-induced damage in the case of small clearances. The analytical method for estimating the wave forces on the box-girder superstructure of coastal bridges is proposed based on the potential flow theory in this paper. The two-dimension problem of the box-girder superstructure under the wave action is defined with some necessary simplifications first. Then, the analytical solutions are solved by the eigenfunction matching method, and the wave force on the submerged box-girder superstructure is calculated using the Bernoulli principle. After validating the accuracy of the proposed method by previous calculations and the experimental test, the influences of the girder type and structural configuration on the wave forces of submerged box-girder are conducted using the proposed analytical method. The results show that the girder type has a significant effect on the wave forces of the submerged superstructure, and the influence of various structural parameters should be considered comprehensively in the structural safety design under wave actions. The results of the present study can provide a useful reference for the estimation of wave forces and the structural design of the box-girder superstructure of coastal bridges.