Quantification of rhizodeposition (root exudates and root turnover) represents a major challenge for understanding the links between above-ground assimilation and below-ground anoxic decomposition of organic carbon in rice paddy ecosystems. Free-air CO2 enrichment (FACE) fumigating depleted 13CO2 in rice paddy resulted in a smaller 13C/12C ratio in plant-assimilated carbon, providing a unique measure by which we partitioned the sources of decomposed gases (CO2 and CH4) into current-season photosynthates (new C) and soil organic matter (old C). In addition, we imposed a soil-warming treatment nested within the CO2 treatments to assess whether the carbon source was sensitive to warming. Compared with the ambient CO2 treatment, the FACE treatment decreased the 13C/12C ratio not only in the rice-plant carbon but also in the soil CO2 and CH4. The estimated new C contribution to dissolved CO2 was minor (ca. 20%) at the tillering stage, increased with rice growth and was about 50% from the panicle-formation stage onwards. For CH4, the contribution of new C was greater than for heterotrophic CO2 production; ca. 40–60% of season-total CH4 production originated from new C with a tendency toward even larger new C contribution with soil warming, presumably because enhanced root decay provided substrates for greater CH4 production. The results suggest a fast and close coupling between photosynthesis and anoxic decomposition in soil, and further indicate a positive feedback of global warming by enhanced CH4 emission through greater rhizodeposition.