Given the research situation of toxic metals (TMs) pollution in farmland soil, it is very critical to study the clay influence on TMs environmental behavior to meet the aim of lowering TMs pollution. This research explores the association among clay minerals and TMs and the health risks in TMs combined polluted farmland of northern China. In this study, agricultural soil, wheat grain, and atmospheric sediments from nonferrous metal smelting (NMS) areas were collected and investigated to determine the effect of clay minerals on TMs. The results show that the content ranges of Cd (0.199 mg/kg ∼1.98 × 102 mg/kg), Pb (0.228 × 102 mg/kg ∼ 4.87 × 103 mg/kg), Cu (0.187 × 102 mg/kg ∼ 4.57 × 103 mg/kg), and Zn (0.559 × 102 mg/kg ∼ 3.04 × 103 mg/kg) in the agricultural soil. In particular, Cd has reached heavy pollution by the high pollution index (6.74). The findings indicate that Cd and Pb in wheat grain were influenced by their exchangeable fractions in soil, according to a significant relationship between Cd and Pb in soil and wheat grain. XRD-SEM suggests that TMs come from atmospheric sediments associated with NMS emissions by microsphere signatures with surface burn marks. Meanwhile, Geographical detector indicated that clay was the primary contributor to spatial distribution of Cd and Pb. In addition, XRD results showed that I/S (a mixed layer of illite and smectite), illite, chlorite, and kaolinite co-existed. Whereas the clay minerals with this ratio did not demonstrate better adsorption capacities for Cd and Pb due to the Cd percentage of the residual fraction being less than 9%. The result of negative correlation between exchangeable Cd and clay minerals implies that illite, chlorite, and kaolinite may preferentially adsorb Cd and Pb. It is similar to the relationship between Cd and Pb in wheat grain and illite, chlorite, and kaolinite. In addition, the health assessment result show that the negative correlation between clay minerals and the noncarcinogenic hazard quotient (HQ) and indicate that clay minerals could reduce the noncarcinogenic risk of Pb and Cd for children. Our findings provide a potential mechanism and application of clay minerals for the remediation of soil contaminated with TMs.