High-resolution topographic data acquired by remote aerial vehicles (RAVs) have facilitated the use of digital elevation model (DEM) and DEM of difference (DoD) methods for studying geomorphic processes in complex terrain. However, insufficient understanding of systematic bias and random errors for DEMs constrained the application. In this study, we comprehensively analyzed the spatial pattern and magnitude of errors (including systematic and random errors) of DEMs derived from RAV-acquired point clouds for a topographically complex area (a subcatchment of Qiaogou in the hilly and gully loess plateau (SC_QG), China). The relationships between random errors and influential factors associated with topography, point cloud density, vegetation, and interpolation algorithms were also evaluated. On this basis, an error source thresholding (EST) method was adapted through incorporating residual systematic errors and including more impacting factors in the fuzzy inference system for random error estimation. The adapted EST (AEST) method was then employed to quantify the DoD uncertainty and geomorphic changes in two small catchments with complex terrain (i.e., SC_QG and a sub-catchment of Telagou (SC_TLG) in the hilly and gully Loess Plateau, China), while the results were verified by the changes measured by terrestrial laser scanning (TLS) and erosion pins, respectively. Results showed that mean value of systematic errors of DEMs were 0.065 and 0.005 m for SC_QG and SC_TLG, while the residual errors were reduced to 0.002 and 0.001 m after co-registration, respectively. Significant statistical relationships (p< 0.01) were found between random errors and influential factors. The erosional volume of two study sites detected by the adapted method were -252.29 and -981.07 m(3) and the corresponding depositional volume were 30.57 and 1594.32 m(3), respectively. The adapted method achieved a comparable pattern and magnitude of volumetric changes with TLS results, which was superior to the original EST method in SC_QG. Besides, our method showed a lower absolute error (0.034 m) compared to the original method (0.087 m) through a comparison with erosion pins measurement in the SC_TLG. Overall, the AEST method provided a reliable tool for geomorphic change detection in areas associated with complex terrain.