Although fertilization of controlled-release fertilizer (CRF) and crop rotation have been shown the contribution to improving yield, nutrient use efficiency, and soil fertility, their interactions on the quality of relcalimed land remains unclear. Hence, a field experiment was conducted in a reclaimed land along Yangze River to investigate their interactions. Results indicated that application of bulk blending urea (BBU) of conventional urea and controlled-release urea (CRU) with appropriate dosage and frequency increased the rice yield and nitrogen agronomic efficiency (NAE). Crop rotation also improved the rice yield and NAE through enhancing the retention capability of fertility. Crop rotation combined with fertilization significantly increased the soil pH, organic carbon (SOC), total N (TN), and permanganate oxidizes carbon (POXC). The rice-green manure (RG) rotation improved soil pH and TN most, and the rice-rape (RR) rotation improved SOC most. Fertilization of conventional urea and BBU both significantly increased the labile SOC functional groups and reduced the the stabled SOC functional groups under RG rotation. Under RR rotation, however, only fertilization of conventional urea increased the labile SOC functional groups and reduced the the stabled SOC functional groups. The rice-wheat (RW) rotation showed no significant effects on the changes in soil organic functional groups. The changes in soil properties had significant effects on improving rice yield or NAE under RG and RR rotations instead of RW rotation. The findings suggested that BBU combined with crop rotations could make good use of reclaimed land through improved nutrient use efficiency and soil fertility.