Global warming is an increasingly serious ecological problem, we examined how the active autotrophic microbes in paddy soils respond to the elevated CO₂ and temperature. Here we employed stable isotope probing (SIP) to label the active bacteria using the soil samples from a fully factorial Simulated Climate Change (SCC) field experiment where soils were exposed to ambient CO₂ and temperature, elevated temperature, elevated CO₂, and both elevated CO₂ and temperature. Around 28.9% of active OTUs belonged to ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). Nitrosospira taxa was dominant in all soils and 80.4% of carbon-fixing bacteria under elevated temperature were classified as Nitrosomonas nitrosa. While no labeled NOBs were detected when temperature or CO₂ were elevated independently, diverse NOBs were detected in the ambient conditions. We found that elevated CO₂ and temperature had contrasting effects on microbial community composition, while relatively small changes were observed when CO₂ and temperature were elevated simultaneously. Summarily these results suggest that carbon-fixing bacteria can respond positively to elevated CO₂ concentrations, but when it’s accompanied with increase in the temperature this positive response could be weakened. Multiple abiotic factors thus need to be considered when predicting how microbial communities will respond to multiple climatic factors.