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Soil nitrogen (N)‐fixing bacteria community plays an important role in the N cycling process in soil, but there is still limited information about how the soil microbes that drive this process to respond to combined application of tillage and crop residue management under the double‐cropping rice (Oryza sativa L.) paddy field in southern of China. Therefore, the effects of 6‐years short‐term tillage treatment on soil N‐fixing bacteria community under the double‐cropping rice paddy field in southern China were studied by using the polymerase chain reaction‐denaturing gradient gel electrophoresis method. The field experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no‐tillage with crop residue retention (NT), rotary tillage with crop residue removed as control (RTO). The results showed that the diversity index and richness index of cbbLR and nifH genes with CT, RT, and NT treatments were increased, compared with RTO treatment. Compared with RTO treatment, the abundance of cbbLR gene with CT, RT, and NT treatments were increased by 6.54, 4.73, and 2.78 times, respectively. Meanwhile, the abundance of nifH gene with CT, RT, and NT treatments were 5.32, 3.71, and 2.45 times higher than that of RTO treatment. The results also indicated that soil autotrophic Azotobacter and nitrogenase activity with CT and RT treatments were significantly higher (p <.05) than that of RTO treatment. There was an obvious difference in characteristic of soil N‐fixing bacteria community between the application of crop residue and without crop residue input treatments. In summary, the results indicated that the abundance of N‐fixing bacteria community in the double‐cropping rice paddy field increased with conventional tillage and rotary tillage practice. [ABSTRACT FROM AUTHOR]