Unmanned aerial vehicles (UAVs) can obtain high-resolution topography data flexibly and efficiently at low cost. However, the georeferencing process involves the use of ground control points (GCPs), which limits time and cost effectiveness. Direct georeferencing, using onboard positioning sensors, can significantly improve work efficiency. The purpose of this study was to evaluate the accuracy of the Global Navigation Satellite System (GNSS)-assisted UAV direct georeferencing method and the influence of the number and distribution of GCPs. A FEIMA D2000 UAV was used to collect data, and several photogrammetric projects were established. Among them, the number and distribution of GCPs used in the bundle adjustment (BA) process were varied. Two parameters were considered when evaluating the different projects: the ground-measured checkpoints (CPs) root mean square error (RMSE) and the Multiscale Model to Model Cloud Comparison (M3C2) distance. The results show that the vertical and horizontal RMSE of the direct georeferencing were 0.087 and 0.041 m, respectively. As the number of GCPs increased, the RMSE gradually decreased until a specific GCP density was reached. GCPs should be uniformly distributed in the study area and contain at least one GCP near the center of the domain. Additionally, as the distance to the nearest GCP increased, the local accuracy of the DSM decreased. In general, UAV direct georeferencing has an acceptable positional accuracy level.