Lowland rice along with wetland sequesters one third of terrestrial carbon (C) which is responsible for both positive and negative feed-back to climate change. Labile C pools are sensitive to anticipated climate change condition (elevated CO2 and temperature). Those may eventually affect the C-stock in soil-microbes-plant-atmospheric (SMPA) continuum through priming effect and could enhance positive climate change feedback. Therefore, the objectives of the study were to analysis the effect elevated CO2 on C partitioning in rice-plant parts, soil labile C pools, and methane emission; along with identify related bacterial diversities and C-fixation pathways through whole genome metagenomic approach. The labile carbon flow in SMPA continuum was estimated for 3 years in lowland rice under elevated CO2 and temperature in open top chambers (OTCs). Rice was grown under ambient CO2 (a-CO2; 390 ± 20 μmol mol−1) and elevated CO2 and temperature (e-CO2T; 550 ± 20 μmol mol−1; 2 °C above ambient) under OTCs with replications. Soil labile C pools were increased by 25.4 to 38.9%, under e-CO2T over a-CO2. In microbes, biomass C, C-fixation pathways (metagenomic analysis) and C related soil enzymes were assayed. In atmosphere, the methane emission was measured and in plant system, C in different plant- parts, photosynthetic rates, root exudates-C were estimated to quantify labile C flow. Root exudates C was increased by 31.9% and microbial biomass C was enhanced by 23.3% under e-CO2T. Primarily, 12 soil bacterial genera which were responsible for C-fixation were dominant with higher abundance reads under e-CO2T. In C-fixation, dicarboxylate hydroxybutyrate cycle pathway and reductive citric acid cycle pathway were predominant under a-CO2 and e-CO2T, respectively. The methane emission was 26.0 and 26.8% higher under e-CO2T than a-CO2 at vegetative and reproductive stage of crop, respectively. Further, we got higher biomass accumulation, photosynthetic rate and stomatal conductance of rice under e-CO2T. Therefore, these augmented labile C flows in SMPA continuum may trigger the priming of soil C stocks, and at the same time could affect the system as a whole and results a positive feedback to climate change.