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Controlled release fertilizer can reduce nitrogen losses to the environment while increasing grain yield and improving apparent nitrogen recovery (ANR) of rice. However, few studies have evaluated the comparative efficacy of different polymer-coated urea products on nitrogen (N) losses, ANR, and N uptake of rice. A 2-year field experiment was conducted to compare the effects of three different types of polymer-coated urea fertilizer on nitrogen losses through NH volatilization and surface runoff to the environment, ANR, grain yield, and N uptake as compared to conventional urea of rice. Six treatments including (1) control with 0 kg N ha (CK), (2) basal application of urea (U), (3) split application (U) of urea (50% at transplanting, 25% at tillering, and 25% at panicle stages), (4) CRU-1 (polyurethane-coated urea), (5) CRU-2 (degradable polymer-coated urea), and (6) CRU-3 (water-based polymer-coated urea) all applied at 165 kg N ha. It was found that CRU-2 resulted in the highest grain yield and panicle numbers among the N fertilization treatments in 2013 and 2014. Applying CRU could help increase N uptake in rice, reduce N losses through NH volatilization and surface runoff, and hence improve ANR. Its single dose can meet the nutrient demand of the rice plant. Controlled release urea could be adopted as an effective mitigation alternative to retard N losses through NH volatilization and surface runoff while improving ANR of double cropping of late rice.