This study investigates the spatiotemporal variations and influencing factors of topsoil heavy metals in the Pearl River Basin by utilizing data from the 2000s to the 2010s obtained from China Geochemical Baselines project (CGB1: 2008-2012
CGB2: 2015-2019), alongside geostatistics methods and a modified absolute principal component scores-multiple linear regression (APCS-MLR) model. The results indicate that the median concentrations of As, Cd, Pb, Zn, Cu, Cr, Ni, and Hg exhibited a decreasing trend from the CGB1 to CGB2. Notably, As concentrations decreased the most, with a reduction percentage of 24.7%. Mining and smelting activities predominantly influenced the concentrations of As, Cd, Pb, Zn, and Cu, which decreased respectively from 16.34 mg/kg to 12.31 mg/kg, 365.11 μg/g to 287.38 μg/g, 41.31 mg/kg to 34.20 mg/kg, 96.41 mg/kg to 84.00 mg/kg, and 28.63 mg/kg to 25.72 mg/kg. The contribution rates of these activities ranged from 49.7% to 95.2%. In contrast, natural factors such as parent materials, weathering processes, and soil properties predominantly governed the concentrations of Cr and Ni, which decreased respectively from 62.03 to 55.92 mg/kg and 23.74 to 22.98 mg/kg, with contribution rates of 42.8% and 71.2%, respectively. Geochemical processes controlled the concentrations of Hg, which decreased from 115.75 to 112.85 μg/g, contributing 62.9%. Given the diverse geology and economic development of the Pearl River Basin, investigations into the spatiotemporal variations and influencing factors of heavy metals in topsoil not only provide a scientific basis for partitioned studies on pollution dynamics and health assessments within the basin, but also establish a foundation for analyzing environmental changes and developing policies in other regions.