China stands as one of the world’s largest agricultural powerhouses, boasting abundant crop resources. Nonetheless, there remains a lack of clarity regarding the extensive scale of crop residue return in the fields. Drawing from direct field measurements and comprehensive survey data, this paper pioneers the reporting of residues from the five primary crops, shedding light on the associated nutrient components, including carbon (C), nitrogen (N), and phosphorus (P) replenishment via crop roots, stubble, and straw in the Southwest China region for the year 2012. The results showed that the total amount of the main crop residue resources was 97.4 Mt, which was composed of 17.8 Mt, 12.6 Mt, and 67 Mt for crop root, stubble, and straw, respectively. After crops harvested, there were 7165.8 kilotonne nutrient C, 132.2 kilotonne nutrient N, and 9.8 kilotonne nutrient P of crop residues returned to the fields through crop root, respectively, accounting for 44.6%, 48.2%, and 43.4% of the total nutrient returned, which was the main part of crop nutrients return to fields. The amount of nutrient C, N, and P returned through stubbles were 5017.3 kilotonne, 75.9 kilotonne, and 6.8 kilotonne, respectively, accounting for 31.3%, 27.6%, and 30.6% of the total return of crops. From the composition proportion of residues nutrients return to field, the orders were all expressed as follows: root > stubble > straw. According to the optimum fertilization amount of the main crops in Southwest China, the returned of crop residues nutrient N in maize, rice, rapeseed, and wheat can replace approximately 5.6%, 18.4%, 11.2%, and 14.8% of nitrogen fertilizer, and 2.4%, 8.3%, 3%, and 9.2% of phosphate fertilizer, respectively. This conclusion is beneficial for regulating the practice of returning crop residues to the fields and the use of agricultural fertilizers, aiming to achieve sustainable development in agricultural production.