The purpose of this study was to investigate the effect of nutrient management practices on crop productivity, energy use efficiency (E-R), greenhouse gas (GHGs) emissions, and carbon (C) and economic yields which impacts the net ecosystem economic budget (NEEB) of worlds' largest rice-wheat cropping system. The effect of different nutrient management strategies (viz. UF control, N, NP, NK, PK, NPK, FYM, N + FYM, and NPK + FYM) on nutrient (N, P, and K) availability, nutrient use efficiency, and yield-scaled global warming potential (GWP) was studied to estimate the environment and economic costs, while increasing E-R in a rice-wheat cropping system. Balanced fertilizer application (NPK) significantly (p < 0.05) improved nutrient uptake and nutrient use efficiency due to increased nutrient availability in soil compared with their imbalanced application. Physiological efficiencies of N, P, and K (PEN, PEP, and PEK) of 78.3, 218.8, and 127.1 kg rice grains per kilogram plant N, P, and K, respectively, were equivalent to their reciprocal internal use efficiencies (RIUE) of 11.6 kg for N, 5.7 kg for P, and 10.4 kg for K to produce 1 Mg grains. In wheat, RIUEN, RIUEP, and RIUEK were 7.9 kg for N, 3.8 kg for P, and 6.7 kg for K to produce 1 Mg grains, against PEN, PEP, and PEK of 121.4, 254.3, and 109.0 kg grains per kilogram plant N, P, and K, respectively. The GWP varied between 10.4 and 13.6 Mg CO2e ha(-1) year(-1), lowest in UF control and the highest with NPK + FYM application. The highest carbon efficiency ratio (CER) under NPK + FYM suggested higher potential to fix C per unit loss. Energy intensiveness (EI) increased by 7.3 MJ US$(-1) and 27.6 MJ US$(-1) with NPK + FYM, respectively, over NPK and FYM alone because of highest net energy gain (NEG). Manure application resulted in higher specific energy (E-S) and lower energy productivity (E-P) compared to application of inorganic fertilizers. The NPK + FYM application increased the C yields, nutrient use efficiency, and the economic efficiency of rice and wheat. Fertilizer application significantly increased the NEEB of rice-wheat cropping system.