Manure substitution shows promise for nitrogen (N) management, food security, energy balance and environmental costs reduction. However, there is limited research on this practice in the Huanghuaihai Plain. This study aimed to investigate the energy use efficiency, economic benefits, carbon and nitrogen footprint under two types of N fertilizer (U, urea and M, organic manure), two application rates of N (180 kg N ha−1, U1 for 100 % urea and M1 for 100 % organic manure; 90 kg N ha−1, U2 for 50 % urea and M2 for 50 % organic manure) and no fertilizer application treatment (CK) for winter wheat from 2017 to 2019. Results showed that grain yield and agricultural input cost under N application rate of 90 kg N ha−1 was 15.5 % and 7.8 % lower than that of 180 kg N ha−1, respectively, leading to a significant decrease in economic benefit. Under the same N rate, M1 obtained higher grain yield than U1, grain yield of M2 did no differ in that of U2. Total energy inputs and agricultural input costs of M were 9.5 % and 3.6 % lower than U, resulting in higher energy use efficiency and economic benefit. The reduced agricultural input for M was primarily due to a decrease in the application of inorganic fertilizer. Compared with other treatments, U2+M2 obtained higher grain yield, energy use efficiency, and economic benefit. The carbon and nitrogen footprint on unit grain yield of U1 was increased by 13.7 %-24.1 % and 3.9 %-19.6 %, which was attributed to the increase in direct N2O emissions, indirect carbon emission and losses of reactive N from agricultural inputs. Overall, U2+M2 sustained high productivity and reduced the environmental impact. Substituting inorganic fertilizer with organic manure was a promising strategy to improve agricultural production with less agricultural inputs and environmental footprints in the Huanghuaihai Plain.