The activity and fate of heavy metals (HMs) from mining and smelting activities in farmland soil is of great significance to effectively prevent the excessive enrichment of HMs in crops. This study focuses on Baiyin area, a typical mining city in northwest China. In this example, the sources, speciation, and fate of HMs in the farmland soil, and the migration and enrichment characteristics of HMs in the different parts of crops planted in different areas were studied in detail combining the chemical sequential extraction and Pb isotope approaches. Results showed that the mean anthropogenic contributions of HMs in farmland soils were approximately 85%, 88%, 76%, and 41% for the ore district (OD), Xidagou sewage irrigation area (XSIA), Dongdagou sewage irrigation area, and the Yellow River irrigation area, respectively, and the risk that HMs were excessively accumulated in crops in OD and XSIA was high. Compared with soil residual fractions, the isotope ratios ²⁰⁶Pb/²⁰⁷Pb in non-residual fractions (1.1304–1.1669) were closer to the values of local ores, suggesting that anthropogenic HMs from mining and smelting activities were mainly enriched in the non-residual fractions. The isotope ratios ²⁰⁶Pb/²⁰⁷Pb in crops (1.1398–1.1686) further confirmed that those anthropogenic HMs were more easily absorbed and concentrated by crops. HMs contents in leaves from OD and XSIA were generally higher than that in roots, suggesting that atmospheric deposition in OD and XSIA had a greater impact on the HMs concentration of crop leaves，while the excess rate of HMs in grain/fruit was the lowest in all parts of crops. The division and classification of crop planting in mining area can effectively help minimize the risk that HMs from anthropogenic source enter the human body through the food chain.