The refraction phenomenon causes ICESat-2 nearshore bathymetry errors by deviating seafloor photons’ coordinates. A refraction correction method based on ATL03 photon parameter tracking was proposed to improve the ICESat-2 bathymetry accuracy. The method begins by searching for sea–air intersections using photon parameters. Instead of relying on mathematical operations, it uses logical relations to establish a relationship between the seafloor and the surface, which improves efficiency. Then, a refraction correction model is designed based on Snell’s law for different sea surface fluctuations. This model is clear and suitable for scholars new to refraction correction. The results show the effectiveness of the proposed method since the RMSE is reduced by 1.8842 m~5.2319 m compared with the raw data. Our method has better tolerance than other methods at different water depth ranges.