The uptake by plants from soil is one of the first steps for hexachlorocyclohexane (HCH) isomers to enter the food web. However, the HCH transformation associated with the uptake process is still not well understood. Therefore, a soil−wheat pot experiment was conducted to characterize the HCH transformation during wheat growth using compound-specific isotope analysis (CSIA) and enantiomer fractionation. The results showed that the δ 13 C and δ 37 Cl values of β-HCH remained stable in soil and wheat, revealing no transformation. In contrast, an increase of δ 13 C and δ 37 Cl values of α-HCH indicated its transformation in soil and wheat. A shift of the enantiomer fraction (EF) (−) from 0.50 to 0.35 in soil at the jointing stage and 0.35 to 0.57 at the harvest stage suggested that the preferential transformation of enantiomers varied at different growth stages. Based on the dual element isotope analysis, the transformation mechanism in the soil−wheat system was different from that in wheat in hydroponic systems. The high abundance of HCH degraders, Sphingomonas sp. and Novosphingobium sp., was detected in the α-HCH-treated rhizosphere soil, supporting the potential for biotransformation. The application of CSIA and EF allows characterizing the transformation of organic pollutants such as HCHs in the complex soil−plant systems.