Principal component analysis and composite scores were used to judge the effects of different proportions of organic fertilizer substitution for chemical fertilizer on citrus yield and quality，and to explore the potential of organic fertilizer substitution in reducing carbon emissions in the citrus production cycle，so as to provide a theoretical basis for its scientific fertilizer reduction，reasonable increase in organic fertilizer application and citrus yield and efficiency. In this study，a two-year field trial of 2018—2019 was carried out in the main citrus production area of Fengjie county，Chongqing. Five treatments were conducted:farmers’ conventional fertilization (FP)，optimized fertilizer application (OPT)，optimized fertilizer application + organic alternative nitrogen fertilizer 20% (OPT+N20)，optimized fertilizer application + organic alternative nitrogen fertilizer 30% (OPT+N30)，optimized fertilizer application + organic alternative nitrogen fertilizer 50% (OPT+N50). The results showed that，(1)Compared with FP，optimized fertilization and organic-inorganic application treatments increased the yield of navel orange and improved fruit quality. There was no significant difference in yield among treatments in 2018. In 2019，the yield of OPT，OPT + N20，OPT + N30 and OPT + N50 were 22.3%，27.3%，28.3% and 34.1% higher than that of FP，respectively. At the same time，the organic-inorganic application significantly reduced the titratable acid，improved the fruit edibility，soluble solids and solid-acid ratio，and also improved the brightness and color of fruit skin compared with FP. (2)Compared with FP，the combined application of organic and inorganic fertilizers significantly increased soil pH and soil available nutrients，and maintained soil nutrient balance. (3)Optimized fertilization and organic-inorganic application significantly reduced greenhouse gas emission intensity and improved economic efficiency compared with FP，and the carbon footprint of organic-inorganic treatment increased by 44.20%，48.10% and 59.23%，and the yield-to-input ratio increased by 63.64%，51.82% and 39.70%，respectively. (4)Through a comprehensive analysis of the yield and fruit quality of navel oranges，the scores of the treatments were ranked as OPT+N30>OPT+N50>OPT+N20>OPT>FP，i.e.，the fertilization response of the organic-inorganic combinations was better than that of the FP treatment，in which the optimal fertilization with organic fertilizer replacing 30% of nitrogen fertilizer had the best effect on fruit quality improvement. The reduction of chemical fertilizer input and organic fertilizer application significantly reduced carbon emission and improved economic efficiency during the production life cycle of navel orange. Therefore，the optimized fertilizer application with organic fertilizer could improve the yield and quality of navel oranges and reduce the carbon emission of orchards.