<p>Crop rotation and straw incorporation play a vital role in N cycling in farmland, yet the impact of their integration on soil N process has not been completely understood. A 3-year experiment on wheat-rice and rapeseed-rice rotations with and without straw return was conducted. Soil N fractions, including the microbial biomass N (MBN), available inorganic nitrogen (Nmin) and soluble organic nitrogen N (DON), fractions associated to the macroaggregates (cPOM), intra-microaggregate (iPOM) and minerals (MOM) were measured. The emissions of N₂O and NH₃ were monitored in yearly cycle. The straw return had greater effects on most of soil N fractions relatively to the rotation modes. When compared to the straw clearing treatment, straw return significantly increased MBN by 17.11%, Nmin by 18.76%, DON by 25.62%, N concentration and partition in iPOM by 31.22% and 5.02%, respectively. The crop N uptakes were greatly enhanced and N₂O emission were significantly reduced with the return of straw. Correlation analysis revealed that MBN and N partition in MOM were closely associated with gaseous N loss and N uptake. Straw incorporation could facilitate N uptake and retention in soil by changing composition of N fractions in rice-based rotations. N partition in MOM and MBN fractions are suggested as potential indicators for paddy N cycle management in subtropical regions.</p>