【Objective】To address the limited understanding of the nutrient stoichiometric relationships among crops, soil, and microorganisms under different proportions of organic fertilizer substitution for chemical fertilizers in a rice-wheat rotation system.【Method】 This study utilized a five-year field experiment at the Yixing experimental site of the Changshu Agro-Ecological Experimental Station, Chinese Academy of Sciences, five treatments were established: no phosphorus fertilizer (CK), conventional chemical phosphorus fertilizer (CF), 30% substitution of chemical phosphorus fertilizer with organic fertilizer (TM), 50% substitution (FM), and 100% substitution (HM). The aim was to investigate the effects of organic fertilizer substitution on crop-soil-microorganism stoichiometric ratios and phosphorus availability under equivalent nitrogen, phosphorus, and potassium inputs. 【Result】Results from ten consecutive cropping seasons over five years revealed no significant differences in the grain and straw yields of rice and wheat or in the total carbon, nitrogen, and phosphorus stoichiometric ratios among treatments. The stoichiometric ratios of available nutrients in soil, including dissolved organic carbon: available nitrogen, dissolved organic carbon: available phosphorus, and available nitrogen: available phosphorus, ranged from 7.08-7.39, 23.1-26.8, and 3.59-4.06, respectively, under the TM, FM, and HM treatments. Compared with CF, these treatments did not significantly alter the total nutrient stoichiometric ratios in the soil but significantly increased the soil organic phosphorus fractions (by 49.7%-58.2%, dominated by moderately labile organic phosphorus, NaOH-Po). Additionally, soil microbial biomass carbon (MBC), nitrogen (MBN), and phosphorus (MBP) in soil increased by 14.3%-61.1%, 4.37%-36.2%, and 46.4%-50.8%, respectively. The microbial stoichiometric ratios under all treatments were as follows: MBC:MBN (11.6-14.5), MBC:MBP (68.3-106), and MBN:MBP (5.32-7.32). The TM and FM treatments significantly reduced the stoichiometric ratio of enzyme activity (EEA(C:N)) but did not affect the overall soil-microorganism stoichiometric balance. 【Conclusion】These findings demonstrate that substituting 30% of chemical fertilizers with organic fertilizers can maintain crop yields while effectively enhancing soil available phosphorus content. This study underscores the critical importance of scientifically regulating the substitution ratio of organic fertilizers to optimize soil nutrient management, improve soil fertility, and promote sustainable agricultural development.