Considerable nitrogen (N) losses from intensive vegetable systems have become an important source of environmental damage. A high-efficiency N application to minimize N pollution and improve production is urgently needed. Here, we conducted field experiments to identify the effects of a single application of controlled-release urea (CRU), conventional urea (CU), and chicken manure (CM) on N losses and yields improvement in a greenhouse tomato system in Beijing, China. Five treatments were carried out: no N control (CK), lower rate of CRU with CU and CM (CRN1), medium rate of CRU with CU and CM (CRN2), higher rate of CRU with CU and CM (CRN3), and conventional fertilization (CN). The results showed that the single application of CRU, CU, and CM reduced the nitrate N concentration and N 2 O emissions by 22 to 79% and 39 to 51%, respectively, compared with the conventional fertilization. Based on the N application rate, the average nitrate N concentration showed an exponential increase, and the cumulative N 2 O emissions showed a linear increase. Compared to the CN treatment, the CRN1, CRN2, and CRN3 treatments decreased fertilization cost by 44%, 22%, and 3.4%, while raising yields by 9.6%, 17%, and 2.0%, respectively. The apparent N surplus of the CRN1 and CRN2 treatments was reduced by 39% and 13% relative to the CN treatment, whereas the CRN3 treatment was as high as that of the CN treatment. It can be concluded that applying CRU, CU, and CM at the higher rate hardly improved the yield but increased the risk of N losses, whereas the lower and medium rates of CRU could reduce N pollution and improve production. The CRN2 treatment, reducing the CRU rate by 25%, with the highest economic efficiency, was the best choice to achieve greater yields with less environmental impacts in greenhouse tomato systems.