Endosulfan is an endocrine disruptor that negatively affects the human central nervous system. Although perennial root vegetable crops have high risks of endosulfan absorption and transfer in soil, safety management studies addressing this problem are lacking. We evaluated endosulfan absorption and transition, as well as plant growth in ginseng cultivation soil, and developed a safety management method for field application. Total endosulfan residual concentrations in the soil and biochar 0.1–1.0% treatment groups were 52–73% after 532 d of spraying, and there was no reduction effect owing to biochar treatment. However, the endosulfan sulfate conversion rate decreased by 21.6–47.1% as the biochar amount increased. Further, there was a 47–95% reduction in the absorption and migration of endosulfan into ginseng in the biochar treatment compared to the control, demonstrating a reduction effect (p < 0.05). Ginseng grown in soil treated with 0.1% biochar showed no growth parameter differences compared to the control (p > 0.05); however, germination rates decreased to <59% when the soil was treated with ≥0.3% biochar. Soil treatment with 0.1% biochar can reduce endosulfan absorption and migration without adversely affecting crop growth. This treatment can be used at the cultivation site, depending on soil conditions.