In the present study, attempts have been made to simulate the effect of climate change on rice growth and yield, under both control and water-stressed conditions. Between the two planting methods, the system of rice intensification (SRI) practice had an advantage for the elevated CO2 conditions, with an additional yield of 1,325 kg ha−1; while it was only 391 kg ha−1 under traditional system of planting rice (TPR). Similarly, the yield decline due to temperature increment was −2.0, −2.4, −6.2 and −12.8 % under SRI practice as compared to that of −4.0, −9.9, −11.3 and −31.7 % in the TPR system for +1, +2, +3 and +4 °C temperature rise, respectively. Thus, doubling of atmospheric CO2 level will compensate for the detrimental effect of increased temperature up to 2 °C in the SRI method of rice cultivation as compared to TPR system of planting. Thus, SRI practice is the most suitable method of rice cultivation under both elevated CO2 and temperature level. Simulation analysis of the present data using the dynamic model, ORYZA2000, indicated that under future adverse climatic conditions, the grain yield showed little variation (+1.83 %) with doubled CO2 at +2 °C temperature rise especially with the water stress situations. However, this could be further raised (+17.10 %) with the supplementation of pink-pigmented facultative methylotroph bacterium (PPFM) bio-fertilizer in the given scenario. Thus, temperature-induced yield alterations especially under water-stressed environment could be favorably mitigated with the CO2 fertilization along with the supplementation of PPFM bio-fertilizer.