To enhance rice yields, synthetic nitrogen (N) fertilizers are often applied in rice paddy fields. Under waterlogged conditions, denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) are the main N transformation processes. However, the effects of long‐term fertilization on the dissimilatory nitrate reduction processes remain largely unclear. Here, we investigated rates of denitrification, anammox and DNRA and the abundance of bacterial and nitrate reduction‐related genes (16S rRNA, narG, nirK, nirS, nosZ and hzsB) in rice paddy fields under different fertilization regimes [i.e., non‐fertilization (CK), NPK fertilization (NPK) and NPK fertilization plus straw returning (NPKS)]. The rates of denitrification, anammox and DNRA in the CK treatment were 46.18, 0.35 and 1.29 nmoL N g−1 h−1, respectively, which were significantly (p < .05) increased by 7.32%–27.78%, 2.45–4.12 folds and 1.01–13.23 folds by NPK and NPKS treatments. This was largely consistent with the increased bacterial and nitrate reduction‐related gene abundances in the NPK and NPKS treatments. In addition, NPKS also significantly increased the relative contribution of DNRA to the total nitrate reduction relative to NPK and CK treatments, indicating that NPKS was more beneficial to N retention in the paddy field. Changes in rates of dissimilatory nitrate reduction processes in response to NPK and NPKS treatments were correlated to variations of soil total N, ammonium contents, pH, soil organic carbon (SOC) contents and nitrate reduction‐related genes, among which SOC contents had the highest explanation. Specifically, fulvic‐like compounds, alkyl C and methoxyl and nitrogen‐alkyl C were the key components determining denitrification, anammox and DNRA rates, respectively. Overall, our study suggests that long‐term NPK and NPKS fertilization stimulate rates of dissimilatory nitrate reduction processes mainly by altering soil C components and NPKS is more effective in maintaining soil fertility in the paddy field.