Flooding and climate warming lead to the increase of low‐molecular‐weight organic acid (LMWOA) inputs to soil. However, it is unclear what the effects of flooding and climate warming on soil nitrogen fraction transformation under LMWOA input are. Fluvisol was collected in the riparian zone of the Three Gorges Reservoir to conduct an incubation experiment with the treatments of three LMWOAs at five contents, two hydrological environments and two temperatures. Compared with LMWOA input of 0 mg kg−1, the soil nitrogen in ion exchangeable fraction (IEF‐N), strong oxidant extractable fraction (SOEF‐N) and non‐transformable nitrogen (NTF‐N) were increased by 35.77, 54.71 and 25.49 mg kg−1, respectively, under LMWOA input of 40 mmol kg−1. Soil nitrogen in the weak acid extractable fraction (WAEF‐N) was decreased by 117.41 mg kg−1. Microbial biomass nitrogen (MBN) was increased by 25.29 mg kg−1, and calcium carbonate (CaCO3) was decreased by 8.03 g kg−1. The contents of IEF‐N, NTF‐N and amorphous iron oxides were higher under the flooding environment than under the drying environment. In contrast, opposite results were observed for soil nitrogen in the strong alkali extractable fraction (SAEF‐N), SOEF‐N and MBN. IEF‐N and NTF‐N contents were higher at 20°C than at 30°C, and the contents of SOEF‐N and MBN were higher at 30°C than at 20°C. WAEF‐N was dissolved by LMWOA through CaCO3 dissolution. The dissolved WAEF‐N was partly transformed into SOEF‐N and NTF‐N by microbial assimilation and humification. Flooding desorbed SAEF‐N through the crystalline transformation of iron oxides. Flooding inhibited the transformation of IEF‐N to SOEF‐N and promoted the formation of NTF‐N, while warming did the opposite. The results provide a perspective of the bound state between soil and nitrogen for understanding the soil nitrogen cycling and help to assess the impacts of climate warming and flooding on soil nitrogen loss from soil to the surrounding water.