Background and Aims <p>Partial organic substitution effectively reduces chemical fertilizer application in orchards and significantly impacts fruit production, soil fertility, and nutrient losses. Yet few studies have evaluated these effects in a unified manner, limiting the comprehensive understanding of the impact of partial organic substitution on orchard sustainability.</p> Methods <p>Using an ecosystem service framework, this study assessed the economic benefits of provisioning (fruit production), regulating (soil carbon sequestration, fertility maintenance, and soil water conservation), and dis-services (N losses) in citrus orchards with a 6-year application of organic/green manure (OM/GM) accompanied by a 30% reduction in chemical nitrogen fertilizer inputs.</p> Results <p>Compared to conventional fertilizer application (CK), both OM and GM maintained citrus yield, improved fruit quality, and significantly increased the value of provisioning services by 36.6% and 26.8%, respectively. Cumulative N₂O emissions, N losses via leaching and runoff were mitigated by partial organic substitution, and OM and GM decreased the value of ecosystem dis-services by 13.6% and 20.7% compared with CK, respectively. Regulating services constituted a relatively small portion of the net ecosystem services value, while GM showed the greatest promoting effect on it compared with other treatments, due to its remarkable role in increasing soil carbon sequestration. Overall, the net ecosystem services value of CK (93.7 × 10³ CNY/ha) was significantly increased to 130.3 × 10³ and 122.2 × 10³ CNY/ha for OM and GM, respectively.</p> Conclusion <p>Partial organic substitution sustains ecosystem services and curbs dis-services, thereby highlighting its beneficial role in the sustainable development of citrus orchards.</p>