The fixation of atmospheric CO2 and N2 by soil bacteria is important to the terrestrial carbon (C) and nitrogen (N) cycles and can be greatly affected by anthropogenic disturbance. The application of mineral fertilizer combined with manure (MCM) instead of MF have been used to mitigate soil degradation caused by long term mineral fertilizer (MF) practiced in widely distributed Moso bamboo. We conducted an investigation, employing the statistical approach of space-for-time substitution, to evaluate the effect of MCM on soil CO2 and N2 fixation bacteria in subtropical region of China. Intensively managed Moso bamboo plantations receiving MCM for 0, 6, 10, 15, and 20 years were examined. MCM management enhanced the content of soil organic C and available soil N, P, K, although some fluctuating values were observed. Soil pH values were generally stable, ranging between 5.0 and 5.5. The abundance of the genes cbbL and nifH decreased significantlyafter 6 years of IM and then gradually recovered. Both CO2 and N2 fixation bacteria have their similar dominant species, such as Bradyrhizobium, but these differed in their relative abundances among treatments. The diversity of both bacterial groups either decreased or increased at the 10-year sampling and later returned to their original levels. The alterations of abundances and measures of community diversity for both CO2 and N2 fixation bacteria were not driven by unique factor. In conclusion, IM practice with MCM in Moso bamboo plantation had an overall positive effect on soil CO2- and N2-fixing bacteria as well as soil properties.