Improving the accuracy of nearshore bathymetric measurements is essential for understanding coastal environments, resource management, and navigation. The Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2) is the first laser satellite that uses the photon-counting technique. The ICESat-2 is equipped with the Advanced Topographic Laser Altimeter System (ATLAS), which enables higher-accuracy measurements of water, ice, and land elevation on Earth. Two-media photogrammetric bathymetry is a type of nearshore bathymetric technology that uses the geometrical characteristics of light rays. With this technique, the accuracy and reliability mainly depend on eliminating systematic errors and ensuring accurate spatial photogrammetric positioning relative to the object being measured. To improve the bathymetric accuracy of two-media photogrammetry, we integrated high-accuracy elevation data from photon datasets as constraining and control parameters. The improved method effectively eliminated systematic errors in two-media photogrammetry during the established joint-block adjustment model. To improve its accuracy and reliability, we employed multispectral WorldView-2 stereo images in our experiments. Furthermore, the bathymetric results were validated and assessed using in situ and photon data. The experimental results show that the highest accuracy achieved with the bathymetric measurements in our study area was a root mean square error (RMSE) of 0.96 m and a mean absolute error of 0.57 m. Using the proposed fusion method, the bathymetric accuracy (as measured using the RMSE) was 1 m higher than that of two-media photogrammetry without the photon datasets.