Controlled-release urea (CRU) is commonly used to improve the crop yield and nitrogen use efficiency (NUE).  However, few studies have investigated the effects of CRU in the ratoon rice system.  Ratoon rice is the practice of obtaining a second harvest from tillers originating from the stubble of the previously harvested main crop.  In this study, a 2-year field experiment using a randomized complete block design was conducted to determine the effects of CRU on the yield, NUE, and economic benefits of ratoon rice, including the main crop, to provide a theoretical basis for fertilization of ratoon rice.  The experiment included four treatments: (i) no N fertilizer (CK); (ii) traditional practice with 5 applications of urea applied at different crop growth stages by surface broadcasting (FFP); (iii) one-time basal application of CRU (BF1); and (iv) one-time basal application of CRU combined with common urea (BF2).  The BF1 and BF2 treatments significantly increased the main crop yield by 17.47 and 15.99% in 2019, and by 17.91 and 16.44% in 2020, respectively, compared with FFP treatment.  The BF2 treatment achieved similar yield of the ratoon crop to the FFP treatment, whereas the BF1 treatment significantly increased the yield of the ratoon crop by 14.81% in 2019 and 12.21% in 2020 compared with the FFP treatment.  The BF1 and BF2 treatments significantly improved the 2-year apparent N recovery efficiency, agronomic NUE, and partial factor productivity of applied N by 11.47–16.66, 27.31–44.49, and 9.23–15.60%, respectively, compared with FFP treatment.  The BF1 and BF2 treatments reduced the chalky rice rate and chalkiness of main and ratoon crops relative to the FFP treatment.  Furthermore, emergy analysis showed that the production efficiency of the BF treatments was higher than that of the FFP treatment.  The BF treatments reduced labor input due to reduced fertilization times and improved the economic benefits of ratoon rice.  Compared with the FFP treatment, the BF1 and BF2 treatments increased the net income by 14.21–16.87 and 23.76–25.96%, respectively.  Overall, the one-time blending use of CRU and common urea should be encouraged to achieve high yield, high nitrogen use efficiency, and good quality of ratoon rice, which has low labor input and low apparent N loss.