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Large-scale topography, such as a seamount, substantially impacts low-frequency sound propagation in an ocean waveguide, limiting the application of low-frequency acoustic detecting techniques. A three-dimensional (3D) coupled-mode model is developed to calculate the acoustic field in an ocean waveguide with seamount topography and analyze the 3D effect. In this model, a correction is introduced in the bottom boundary, theoretically making the acoustic field satisfy the energy conservation. Furthermore, a large azimuth angle calculation range is obtained by using the operator theory and higher-order Padé approximation. Additionally, the model has advantages related to the coupling mode and parabolic equation theory. The couplings corresponding to the effects of range-dependent environment are fully considered, and the numerical implementation is kept feasible. After verifying the accuracy and reliability of the model, low-frequency sound propagation characteristics in the seamount environment are analyzed. The results indicate lateral variability in bathymetry can lead to out-of-plane effects such as the horizontal refraction phenomenon, while the coupling effect tends to restore the abnormal sound field and produces acoustic field diffraction behind the seamount. This model effectively considers the effects of the horizontal refraction and coupling, which are proportional to the scale of the seamount. [ABSTRACT FROM AUTHOR]