Crop rotation between irrigated paddy rice (Oryza sativa L.) and upland soybean [Glycine max (L.) Merr.] (paddy-upland rotation) induces a decline in soil nitrogen (N) fertility, as observed by available soil N. There was a significant negative correlation between the available soil N and the proportion of upland seasons to total crop seasons after the initiation of paddy-upland rotation (upland frequency).The decline in soil N fertility was alleviated by the application of organic materials. Soil total carbon also tended to decrease with an increase in upland frequency. Soil physical properties were affected by the paddy-upland rotation. As soil organic matter decomposed in paddy-upland rotation, the soil density increased with decreasing soil porosity. A suitable range of available soil N for paddy-upland rotation was identified between 80 and 200 mg/kg, the same as for paddy rice. The keys to controlling soil N fertility in paddy-upland rotations are the upland frequency and application of organic materials. To sustain the available soil N over the minimum suitable level of 80 mg/kg, the upland frequency should not exceed approximately 60% when only crop residues and no other organic materials are applied. The upland frequency can be increased by the repeated application of organic materials, thereby maintaining a higher level of available soil N.