Organic pollutants in paddy fields may undergo different processes from those in dryland due to the anaerobic environment. The integrated use of compound-specific stable isotope analysis (CSIA) and enantiomer-specific analysis is a promising technique for understanding the behavior and fate of organic pollutants in soils. In this study, soil samples were collected from paddy fields in three major rice cultivation regions of China, spanning a transect of 4000 km. The mean concentrations of ƩHCHs in paddy soils from the Taihu Plain were the highest (1.44 ng/g). The ratios of α-HCH/β-HCH (all below 11.8) and α-HCH/γ-HCH (92% below 4.64), as well as the enantiomeric fractions (EFs) of chiral α-HCH (mean of 0.81), reflected that the distribution of HCHs was affected by the use of both technical HCHs and lindane. The preferential depletion of (-)-α-HCH and pronounced carbon isotope fractionation of α-HCH (δ13C of −28.22 ± 0.92‰ −23.63 ± 1.89‰) demonstrated its effective transformation. Factors such as altitude, soil temperature, soil pH, soil conductivity and soil organic matter significantly influenced the fate and transformation of HCHs. The current study highlights the integrated application of CSIA and enantiomer-specific analysis to provide multiple lines of evidence for the transformation of HCHs in soils.