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Fertilizers are important for agricultural production because they can effectively promote crop productivity. However, long-term fertilization can cause heavy metal accumulation in soils and crops. This study utilized sequential extraction, the diffusive gradient in the thin films (DGT) technique and risk assessment models to estimate the effects of the longest long-term fertilization (38 years) in China on cadmium (Cd) and arsenic (As) accumulation in soils. The treatments included no fertilization (CK); inorganic nitrogen, phosphorus, and potassium fertilization (NPK); manure fertilization (M); and NPK plus M cofertilization (NPKM). The results indicated that the soils treated with NPKM, M and NPK had significantly increased total and available concentrations of Cd and As after 38 years of long-term fertilization. Cd mainly originates from cattle manure, while As originates from phosphate fertilizer. Sequential extraction results indicated that the application of manure increased the acid/exchangeable fraction (F1) and organic matter-bound fraction (F3) of Cd and As. The risk assessment results showed that the environmental risks of both Cd and As increased during long-term fertilization, and Cd contamination in the soil was at a moderate-high level, while As remained at a relatively low level. According to the calculations of the maximum numbers of years of soil productivity and rice production, Cd was labile and accumulated in the soils, and As was more labile than Cd in terms of accumulating in rice, indicating that the true risk from As in rice is higher than that from Cd. Controlling the heavy metals in fertilizers, mitigating effective amendments, and identifying plant types that accumulate low amounts of contaminants may be good choices for cleaner crop production., (Copyright © 2021 Elsevier Ltd. All rights reserved.)