In agricultural soils, besides anthropogenic sources, diazotrophs are the main source of nitrogen. Effects of temporary climate disturbance and cropping of maize on composition and diversity of nitrogen fixing bacteria in Pachic Udic Argiboroll and Fluventic Ustochrept were examined with the technique of nifH-gene targeted polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) approach combined with advanced statistical analysis, based on soil reciprocal transplantation experiments which were set up along a latitude gradient with distinctly different temperature and precipitation. Both cluster analysis and canonical correspondence analysis (CCA) show that soil properties could be the dominant factor to stimulate variation of diazotrophic composition, whereas temporary climate disturbances also caused a certain extent of differences. Contents of organic carbon and alkali-hydrolyzable N were found to be in significantly positive correlation with Shannon and Simpson indices while pH was in significantly negative correlation. Statistical analysis show that the content of alkali-hydrolyzable N was the determinant variable which explained the differences in diazotrophic composition among all samples (p=0.002). Hydrothermal conditions didn’t have any linear correlation with diazotrophic biodiversity. However, Pachic Udic Argiboroll showed the highest diazotrophic biodiversity while Fluventic Ustochrept showed the lowest under warm temperate climate. In addition, maize plantation increased slightly the diversity of nitrogen-fixing bacterial in all soils, except for in Chao soil in Hailun.