Abstract: In recent years, the planting mode of intercropping watermelon in orchards in the middle and lower reaches of the Yangtze River in China has garnered significant attention. In order to investigate the carbon emission of interplanting watermelon in orchards under different fertilization modes, the study was conducted in a young citrus orchard located at Yitang Town, Hunan Province, three treatments were considered: no fertilizer (CK), chemical fertilizer (NPK), and chemical fertilizer combined with manure (NPKM). It analyzed the difference in the yields and net benefits of intercropping watermelon in the young orchard under the three fertilization regimes. The life cycle assessment (LCA) was performed to evaluate the carbon footprint of the watermelon production system, and to identify the agricultural factors with the highest contribution to carbon emissions under different fertilization regimes. The results showed that compared with CK, the application of the fertilizer significantly increased watermelon yield and greenhouse gas (GHG) emissions, and the net benefit of NPK and NPKM increased by 176.9% and 185.2%, respectively. The total carbon emissions were 1 897.19, 20 682.54 and 19 889.19 kg/hm² (CO₂-eq) for CK, NPK and NPKM, respectively. The production stage of agricultural inputs (e.g. fertilizers) was the main contributor to GHG emissions in the life cycle of watermelon, starting from raw materials to final products. Compared with NPK, the carbon footprint per unit area, per unit yield, and per unit net benefit under NPKM reduced by 30.4%, 28.8% and 32.4%, respectively. The contribution analysis showed that fertilizer production was the primary factor contributing to the carbon footprint of NPK (78.2%) and NPKM (42.9%). In conclusion, considering the carbon footprint and economic benefit, NPKM was better than CK and NPK in intercropping watermelon in young orchards. Also, this study indicated that the fertilizer production technology was one of the key factors restricting the low-carbon emission reduction of watermelon production in the middle and lower reaches of the Yangtze River Basin in China.