Elevated atmospheric CO_2 concentration and temperature may affect nitrifiers and denitrifiers which are related to soil N turnover. A climate change experiment was conducted in the rice-wheat rotation ecosystem. This study was used to investigate effects of elevated CO_2 and temperature on soil microbial community structure, as well as abundance and activity of nitrifiers and denitrifiers. The results showed that no change in the abundance of ammonia-oxidizing bacteria (AOB) and denitrifier was observed at the tillering stage, however at the later stages, elevated CO_2 alone significantly increased the abundance of ammonia-oxidizing archaea (AOA) and denitrifier but there were no changes under CW treatment. The analysis of T-RFLP profiles showed that elevated CO_2 and temperature had no obvious effect on community structure of AOA, AOB or denitrifier, but altered diversity index (H′) of AOA and denitrifier. Moreover, elevated CO_2 alone significantly increased nitrifying rate at the ripening stage. Elevated CO_2 and temperature did not result in significant change in denitrifying rate at each single stage. These results suggested that effects of elevated CO_2 and temperature on microbial community were different among the tillering, heading and ripening stages, and functional microorganism responded differently to multiple climate change treatments.