Studying the effects of the positioning application of mushroom residues on carbon and nitrogen in soil aggregates of paddy field is significant for the reasonable utilization of the mushroom residues and the sustainable development of agriculture, and it can provide theoretical bases for revealing the influence mechanism of the application of mushroom residues on the formation and evolution of soil fertility in paddy field. The soil organic carbon and total nitrogen of soil and soil aggregates at different sizes were studied by collecting soils with different dosage mushroom residues, and the contribution rates of soil aggregates to soil organic carbon and total nitrogen were analyzed. The results showed that the content of soil organic carbon was 4.07%–15.71% higher than that of the control respectively. The contents of soil organic carbon in the treatments with medium and high mushroom residues were 13.27 g/kg and 12.81 g/kg, respectively. The soil total nitrogen content with mushroom residues was 1.75%–8.61% higher than that of the control (P>0.05), and the content of soil total nitrogen with medium and high mushroom residues were 1.47 g/kg and 1.43 g/kg, respectively. In general, the carbon and nitrogen contents of >1 mm soil aggregates were significantly higher than those of other size aggregates. It showed that carbon and nitrogen were mainly distributed in the larger size aggregates. The recovery rates of organic carbon and total nitrogen in different size aggregates were 77.05%–87.36% and 77.66%–89.68%, respectively. The results were reliable and could indicate that mushroom residue could increase the contents of organic carbon and nitrogen of water stable aggregates, could improve soil aggregate structure, and thus was an effective measure to improve the productivity of paddy soil.