Fertilization methods significantly affects sustainability of agricultural production through controlling nutrient efficiency and related environmental emissions as well as energy and economic performance at crop cultivation and fertilizer production stage. Therein, controlled-release urea (CRU) use has been proved to raise nitrogen use efficiency and reduce some nitrogen-related environmental emissions. However, related studies have not been found to address whether CRU can promote coordinated development of crop production based on the energy efficiency, carbon emission intensity, environmental performance and economic benefit from this fertilizer production to crop plantation, which could affect reasonable utilization of CRU due to prejudiced conclusions based on inadequate decision-making information derived from one or two or three aspects abovementioned. To this end, this study proposed a set of evaluation system, composed of energy efficiency, carbon emission intensity, and emergy-based environmental performance through integrating environmental emissions’ impact as well as economic benefit, to investigate the coordinated development of rice production with different fertilization schemes composed of altering ratios of CRU to common urea (CU). In doing so, we attempt to search for the relative balance between long-run sustainability of crop production and short-term gains of stakeholders. The presented approach was applied to a study case, from Sichuan Province, China, based on three fertilization schemes, i.e., N1 (single CU), N2 (single CRU), and N3 (blend application of 60% CRU and 40% CU) with the expanded analysis boundary from N fertilizer production to its application in rice plantation. The results indicate that: (1) relative to N1, introduction of CRU increases energy efficiency by 33.15% and 53.09% for N3 and N2 respectively in terms of kJ/kg rice, production efficiency by 0.85% and 3.39% for N3 and N2 respectively in terms of Adjusted emergy yield rate, and economic benefit by 14.53% and 17.95% for N3 and N2 respectively in terms of Benefit-cost ratio, or increased by 15.87% and 26.98% for N3 and N2 respectively in terms of Adjusted benefit to cost ratio, mainly derived from improving N use efficiency and saving labor; (2) introduction of CRU weakens resource structure by 0.98% and 3.23% for N3 and N2 respectively, and raises environmental load by 0.31% and 2.51% for N3 and N2 respectively due to enlarging share of purchased non-renewable resources and promoting methane emission respectively; (3) introduction of CRU enhances environmental sustainability by 0.27% and 0.55% for N3 and N2 respectively relative to N1, and (4) generally N2 realizes the best coordinated development, followed by N3 and N1. Improving resource structure and mitigating carbon emissions should be emphasized when popularizing CRU use in rice production.