Background: Excessive application of chemical fertilizer has resulted in lower nitrogen uptake and utilization efficiency of crops, decreasing soil fertility, increasing greenhouse gas emissions, and worse environment pollution. Organic material retention is regard as the key to solve these problems. he objective of this study is to conduct an assessment of carbon budget under Astragalus sinicus L. and rice straw retention combined with reduced mineral fertilizer based on the two-year field experiment in a paddy field in the south of China. The experiment was randomized complete block design including four treatments with triplicates: control CK (winter follow, 120 kg ha-1 N fertilizer for each rice season) and three treatments with Astragalus sinicus L. and rice straw retention named RA, RB, and RC (reduced N fertilizer by 15%, 27.5%, and 40% in each rice season). Results: Treatments RA, RB, and RC increased greenhouse gases emissions by 9.30%~101.25%, among which CH4 accounted for more than 60%; Carbon input of crops from treatments RA, RB, and RC increased by 2.25%~12.10% compared with control CK over the two years. Though treatments RA, RB, and RC enhanced CO2 emissions, however, treatment RB decreased carbon footprint and became carbon sink.Conclusions: The results of this study reveal that treatment RB (Astragalus sinicus L. and rice straw retention with reduced N fertilizer by 27.5%) is better in reducing chemical fertilizer amount, increasing crop yield and carbon input, which is more conductive to sustainable development of agriculture.