[Objective] In China, upland-paddy rotation systems are mainly distributed in the Yangtze River Basin, with rapeseed-rice (RR) and wheat-rice (WR) rotations being the main systems. It was noticed that rice productivity varied with the rotation system. Therefore, a long-term experiment, designed to have different treatments concerning rotation system and fertilization pattern, was carried out. The study aimed to explore differences in soil nutrients and distribution of aggregate carbon and nitrogen between RR and WR rotations and between different fertilization methods. It is hoped that the study may providing a scientific basis for optimizing the paddy-upland rotation systems and the fertilization methods as well in the rapeseed-wheat interlaced area of the middle reaches of the Yangtze River.[Method] The field experiment was designed to have two treatments in rotation system (i.e., RR and WR) and three treatments in fertilization, i.e., CK (no fertilization), NPK (chemical fertilization), and NPK+S (chemical fertilization combined with straw returning). Soil samples were collected from the 0-20cm soil layer of each treatment after harvest of the upland crops of the fourth year for analysis of physical and chemical properties, such as soil organic matter, nutrient content, porosity, distribution and stability of soil aggregates, and contribution rate of soil aggregate organic carbon and nitrogen to the soil total.[Result] Compared with WR, RR was 13.1%-19.2% and 18.8%-59.5% higher in content of soil organic matter and available phosphorus when fertilized. Treatment NPK+S was 28.1% than CK and 29.2% higher than Treatment NPK in content of soil total nitrogen. In the group of Treatment NPK, Treatment RR was significantly or 8.1% (in CK) and 10.3% (in Treatment NPK) higher and 11.7% and 10.5%, respectively, higher than Treatment WR in total porosity and capillary porosity. In the group of fertilization treatments (either NPK or NPK+S), Treatment WR was significantly higher than Treatment RR in mean weight diameter (MWD) and geometric mean diameter (GMD) of the water-stable soil aggregates and content of water-stable macroaggregate (WSMA), and in contribution rate of large-sized soil aggregates to total organic carbon and total nitrogen as well. In terms of soil organic matter and nutrient contents the fertilization treatments displayed an order of CK < NPK < NPK+S, and Treatments NPK and NPK+S were significantly higher than CK in soil aggregate stability and contribution rate of large-sized aggregates to total organic carbon and total nitrogen, regardless of rotation patterns. In the group of Treatment WR, Treatment NPK + S was significantly higher than CK and NPK in soil total porosity and capillary porosity, while in the group of Treatment RR, no significant difference was observed in soil porosity between different fertilizer treatments.[Conclusion] All the findings show that under the rapeseed-rice rotation system, application of chemical fertilizer combined with straw returning can increase contents of soil organic matter and soil nutrients, improve bulk density and porosity of the soil, and stabilize soil aggregate structure. Hence, the combination of rapeseed-rice rotation and application of NPK coupled with straw returning could be deemed as an important measure to achieve sustainable development of rice fields.