The rapid, up-to-date, cost-effective acquisition and tracking of intertidal topography are the fundamental basis for timely, high-priority protection and restoration of the intertidal zone. The low cost, ease of use, and flexible UAV-based photogrammetry have revolutionized the monitoring of intertidal zones. However, the capability of the RTK-assisted UAV photogrammetry without ground control points, the impact of flight configuration difference, the presence of surface water in low-lying intertidal areas on the photogrammetric accuracy, and the potential of UAV/satellite Synergy remain unknown. In this paper, we used an RTK-assisted UAV to assess the impact of the above-mentioned considerations quantitatively on photogrammetric results in the context of annual monitoring of the Chongming Dongtan Nature Reserve, China based on an optimal flight combination. The results suggested that (1) RTK-assisted UAVs can obtain high-accuracy topographic data with a vertical RMSE of 3.1 cm, without the need for ground control points. (2) The effect of flight altitude on topographic accuracy was most significant and also nonlinear. (3) The elevation obtained by UAV photogrammetry was overestimated by approximately 2.4 cm in the low-lying water-bearing regions. (4) The integration of UAV and satellite observations can increase the accuracy of satellite-based waterline methods by 51%. These quantitative results not only provide scientific insights and guidelines for the balance between accuracy and efficiency in utilizing UAV-based intertidal monitoring, but also demonstrate the great potential of combined UAV and satellite observations in identifying coastal erosion hotspots. This establishes high-priority protection mechanisms and promotes coastal restoration.