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• Net primary production (NPP) as C input source was higher in rice cropping season than fallow season. • Mineralized C loss as C output source was much higher in cold fallow season than warm cropping season. • Net ecosystem C budget (NECB) was negative in the conventional farming system (NPK). • Cover cropping and its biomass incorporation significantly increased soil C stock. In temperate paddy fields, rice is generally cultivated under flooding for 100–140 days during summer season, and thereafter, the soil is left without management under dried soil condition during cold fallow season. In this area rice straw is mostly removed for cattle feeding. Therefore, soil organic carbon (SOC) stock could be decreased with conventional practices, but the seasonal changes of SOC stock have not been evaluated well. To investigate SOC stock changes in temperate rice paddy, two seasonal C balances during rice cropping and fallow season were compared by the net ecosystem C budget (NECB) in the chemical fertilizer (control) and two different green manure treatments for three years. In the control treatment only chemical fertilizer was conventionally fertilized for rice cropping, but maintained without human control during the fallow season. In two green manure treatments, barley and hairy vetch (hereafter, vetch) were cultivated during the fallow season, and their whole biomasses were incorporated before rice transplanting. The conventional soil management with only chemical fertilization decreased small level of SOC stock (minus 0.70–0.84 Mg C ha−1 y−1 of NECB), which was attributed by high harvest removal (approximately 70% of total C input) and mineralized C loss (30%). Cover cropping and its biomass recycling as green manure was effective to increase SOC stock. High C/N ratio of non-leguminous barley produced high biomass yield, and its biomass incorporation significantly increased SOC stock with 1.21–3.43 Mg C ha−1 y−1 of annual NECB. In comparison low C/N ratio of leguminous vetch application increased slightly SOC stock (0.17–1.34 Mg C ha−1 y−1 of NECB), due to low biomass productivity and high mineralized C loss. However, irrespective with fertilization background, approximately 70% of mineralized C loss were occurred during the cold fallow season. Rice grain yields were similar between the control and hairy vetch treatment, but around 10% lower in barley treatment. Conclusively, high C/N ratio of cover crop cultivation during the fallow season could be better to increase SOC stock in mono-rice paddy, but additional nutrient management to increase rice productivity should be developed for barley utilization as green manure. [ABSTRACT FROM AUTHOR]