In real ocean environments, natural reefs typically exhibit complex topography, with reef platforms presenting non-uniform characteristics. Previous extensive research has mainly focused on simplified stepped reef models and has not conducted in-depth studies on the impact of non-uniform reef platforms on the propagation and evolution characteristics of waves. To address the shortcomings of previous research, this paper conducted physical model experiments to systematically study the propagation and evolution characteristics of tsunami-like waves over complex reef platforms. Previous studies did not consider the impact of the non-uniformity of reef platform topography on solitary waves, therefore, this paper also analyzed the effects of incident wave height and reef platform water depth. To investigate the impact of non-uniform reef platform geometric characteristics on the propagation and evolution of tsunami-like waves and the load characteristics of sea walls under different incident wave conditions, this paper further carried out a series of high-resolution numerical calculations. First, physical experiments were used to verify the accuracy of the numerical simulation method, and then numerical calculations were used to study the effects of two wave parameters, incident wave height and reef platform submergence depth, and three complex reef topography factors—the height of the second reef platform, the position of the reef platform steps, and the slope of the reef front slope—on the maximum wave height along the path, reflection coefficient, maximum run-up height, distribution of the maximum impact pressure on the sea wall, and the variation of the maximum total force and total moment on the sea wall. The research results indicate that the reflection coefficient of solitary waves decreases with increasing incident wave height and increases with increasing reef platform water depth. The maximum run-up height increases with increasing incident wave height and decreases with increasing cot α of the reef front slope. The maximum total force and maximum total moment on the sea wall increase with increasing incident wave height and reef platform water depth, and decrease with increasing height of the second reef platform. The position of the maximum impact pressure on the sea wall rises with increasing incident wave height, increasing reef platform water depth, and decreasing distance between the reef platform steps and the sea wall. The research results can provide a reference for further protecting coastal facilities from the impact of extreme marine environments.