To determine the feasibility of planting rapeseed to safely utilize heavy metals (HMs)-contaminated farmlands surrounding working smelters under atmospheric deposition, a field trial was conducted to analyze the yields, cadmium (Cd) and lead (Pb) concentrations, health risks, and economic benefits of 15 rapeseed cultivars (13 Brassica napus L. and two Brassica campestris L.) in Jiyuan City, Henan Province, China. The results show that the seeds’ Cd concentration was 0.12–0.64 mg·kg−1 and the seeds’ Pb concentration was higher than Cd at 0.49–1.22 mg·kg−1. The Cd bioconcentration factor of B. campestris (0.702–0.822) was higher than that of B. napus (0.246–0.502). Additionally, Cd and Pb transfer factors from the stems to the pods and seeds were 0.34–1.20 and 0.54–4.53, respectively. Combined with a comprehensive analysis of the annual deposition data of Cd and Pb, 16.40 and 345.79 kg·hm−2, respectively, HMs in the seeds were not only derived from those in the soil, but were also derived from the atmosphere. Furthermore, the Cd and Pb levels in rapeseed oil, meal, and straw met the requirements stipulated in the standards for food safety, feeds hygiene, and organic fertilizer in China. Rapeseed–maize rotation yielded a profit of 15,550 CNY·a−1·hm−2, thereby increasing the economic output by 133.8%. A cluster analysis revealed that B. campestris SYH and ZS100 and B. napus ZY-821 showed the greatest comprehensive benefits. In conclusion, rapeseed cultivation is a viable and extendable approach that can achieve the safe utilization of typical HMs-contaminated farmland caused by atmospheric deposition in Northern China.