Abstract: The Hexi Corridor is a famous irrigated agricultural area in Northwest China. However, ecological weakness and heavy long-term chemical fertilizer application has caused problems such as low organic matter content, soil structure degeneration, and low crop yield. Returning organic materials into the field is the main solution to improve soil fertility; however, it also risks causing heavy metal pollution in the soil. This study aimed to explore the effect of soil quality and crop yield response to different types of applied organic materials in the field. The long-term positioning experiment consisted of 8 treatments:no fertilizer (CK) as control, conventional fertilizer (NP), 70% conventional fertilizer respectively, with cow dung (0.7NP+NF), with biogas residue (0.7NP+ZZ), with sewage sludge (0.7NP+WN), with chicken manure (0.7NP+JF), with mushroom substrate residue (0.7NP+JZ), and with pig manure (0.7NP+ZF). We studied how partially replacing chemical fertilizers with different organic materials affected the physical and chemical soil properties, soil organic carbon sequestration efficiency, total nitrogen; the activation coefficients of nitrogen, potassium, and phosphorus, as well as crop yield, and heavy metal content. The results showed that the effect of annual applications of organic materials with 70% chemical fertilizer on yield was equivalent to that of NP of wheat and corn. Compared with NP the soil organic matter, total nitrogen, and available nitrogen content significantly increased under six organic materials treatments; the total phosphorus and available phosphorus content of sludge, chicken manure, and pig manure treatments significantly improved; and the available potassium content, soil phosphorus activity, and soil potassium activity of cow manure, biogas residue, and chicken and pig manure treatments also significantly improved. The organic carbon soil sequestration rate of cow dung, biogas residue, sewage sludge, mushroom substrate residue, and chicken and pig manure treatments were 36.42%-71.61% significantly higher than that of NP. While, the nitrogen soil sequestration rate was 6.47%-49.44% significantly higher than NP, except the mushroom residue treatment. Long-term applications of chicken manure and mushroom substrate residue significantly increased the total copper content by 4.17 mg·kg^-1 and 14.2 mg·kg^-1, respectively; sludge, chicken manure, and mushroom substrate significantly increased total content of zinc by 13.53 mg·kg^-1, 22.60 mg·kg^-1, and 49.73 mg·kg^-1, respectively. In conclusion, applications of 4 500 kg·hm^-2organic materials could replace 30% nitrogen and phosphorus fertilizer without reducing the crop yield. The degree that different organic materials affected soil fertilization was varied; sewage sludge, chicken manure, and pig manure were better than cow manure and biogas residue, while mushroom substrate residue was slight worse. When planting wheat, the annual carrying capacity for copper and zinc from organic materials should be less than 53.01 g·hm^-2 and 221.30 g·hm^-2, respectively. When planting corn, the annual carrying capacity of copper and zinc from organic matter should be lower than 153.40 g·hm^-2 and 347.04 g·hm^-2, respectively, to allow soil environmental quality to be stable without deteriorating.