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• A UAV-based method estimating sediment deposited behind check dams was developed. • Errors of the optimal model for single and regional check dams are 12–13% and 2–3%. • This method avoids limitations of tedious field surveys and historical records. • This method can evaluate sediment retained by check dams in areas as large as 211,800 km2. The estimation of sediment deposited behind dams and reservoirs is of great significance for quantifying soil erosion rate and sediment flux. However, existing methods of sediment volume estimation often require detailed field measurements and historical topographic data, limiting the broader application of these methods. In this paper, focusing on the region that suffers the world's most severe soil erosion, we combine unmanned aerial vehicle (UAV) photogrammetry and simulate submerging analysis to propose a novel method for estimating sediment silted by check dams under complex topography. We obtained 1339 groups of topographic factors and ascertained the corresponding volumes of sediment deposited behind check dams in the loess hilly region of China (LHRC), and established five different models combined with regression analysis. Two different sets of data were used for method validation and optimal model determination. The results showed that the error of the optimal model in the volume estimation of single check dam and regional check dams is 12–13% and 2–3%, respectively. Additionally, the area-volume model has the potential to evaluate the sediment retention capacity of check dams (in the order of billions of cubic meters) in the whole LHRC, because the variables are easy to obtain and the model accuracy is relatively high. The further application of this method will help to evaluate the watershed sediment yield and regional soil and water conservation benefits, and is of great significance for explaining the future changes in water and sediment in the Yellow River basin. [ABSTRACT FROM AUTHOR]