Objective Integrated organic-inorganic fertilization proves more effective than chemical fertilizer alone improving the crop growth environment. This study investigated the impact of different fertilization regimes on ecological stoichiometry and system stability in greenhouse soil-crop systems, which was crucial for guiding sustainable agricultural management. Methods A greenhouse experiment with tomato-cucumber rotation was conducted from 2022 to 2023 in Fangshan District, Beijing. Five fertilization treatments were established: T0 (no fertilizer), T1 (chemical fertilizer), T2 (organic fertilizer), T3 (50% chemical fertilizer+50% organic fertilizer), and T4 (50% chemical fertilizer+50% organic fertilizer+amendments). We analyzed 27 parameters, including soil physical properties and rhizosphere microbial community structure, to assess the homeostatic characteristics of the soil-crop system based on ecological stoichiometry. Two triangle models (TR1 and TR2) were employed to calculate system sustainability indices and evaluate the impacts of different fertilization practices on system homeostasis. Results Cucumber plants exhibited strong homeostasis with minimal influence from fertilization treatments. In contrast, soil microbial biomass carbon, nitrogen, and phosphorus were sensitive to fertilization, showing a non-homeostatic state with H (Homeostasis Index)<1.3. System under T3 and T4 treatments achieved a sustainable production level (H≥1.3), whereas T0 and T1 resulted in an unsustainable state (H<1.3). Model analysis confirmed that organic-inorganic fertilization significantly enhanced system sustainability. The amendment in T4 further improved stability by regulating carbon-nitrogen-phosphorus (C-N-P) cycling. The sustainability indices exhibited a significant positive correlations(P<0.01)with soil organic carbon, total nitrogen, and microbial indices. Conclusion The microbial indices exhibited higher explanatory power in the TR2 model, proving to be a more precise indicator of soil ecosystem functional changes. Our findings provided important insights for advancing sustainability in facility agriculture.
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