Fertilization is an effective agronomic management technique for increasing crop production. However, the overuse of chemical fertilizer stimulates energy consumption and greenhouse gas (GHG) emissions, which are antagonistic to sustainable wheat production. In this study, we estimated the energy and GHG performances of different fertilization regimes based on a 32−year fertilization experiment. In this long−term experiment, there are five treatments: CK (no fertilizer with wheat residue removal), NPK (chemical fertilizer with wheat residue removal), NPKPM (chemical fertilizer and pig manure with wheat residue removal), NPKCM (chemical fertilizer and cattle manure with wheat residue removal), and NPKWS (chemical fertilizer with wheat residue retention). The results indicated that NPKCM and NPKPM consumed higher total energy than NPK and NPKWS, which was attributed to the extra energy usage of farmyard manure. Although NPKCM and NPKPM increased energy output by 4.7 and 2.8%, NPKWS stood out by delivering the highest energy use efficiency (EUE) of 6.66, energy productivity of 0.26 kg MJ−1, energy profitability of 5.66, net return of 1799.82 US$ ha−1 and lower specific energy of 3.84 MJ kg−1. Moreover, the yield scale carbon footprint of NPKWS decreased by 66.7 and 52.3% compared with NPKCM and NPKPM, respectively. This study shows that the application of chemical fertilizer in combination with wheat residue retention is a good strategy to increase EUE and economic benefits while decreasing the carbon footprint of wheat production.