Deep fertilization is a beneficial approach for reducing nitrogen losses. However, the effects of various fertilization depths on maize (Zea mays L.) productivity and environmental footprints have not been thoroughly understood. Therefore, a field experiment was conducted to investigate the effects of different fertilization depths of 5 cm (D5), 15 cm (D15), 25 cm (D25), and 35 cm (D35) on maize productivity and environmental footprints. Reactive nitrogen (Nr) losses and greenhouse gas (GHG) emissions were assessed using life cycle analysis. We hypothesized that deep fertilization can obtain lower carbon and nitrogen footprint. The results indicated that deep fertilization decreased the N2O and NH3 emissions while increasing the CH4 uptake. Compared with D5, D15 resulted in an increase in total GHG emissions and carbon footprint (CF), whereas D25 decreased by 13.0% and 23.6%, respectively. Compared with D5, the Nr losses under D15, D25, and D35 conditions was reduced by 11.3%, 17.3%, and 21.0%, respectively, and the nitrogen footprint (NF) was reduced by 16.0%, 27.4%, and 19.0%, respectively. The maize yield under D15 and D25 increased by 5.7% and 13.8%, respectively, compared with the D5 treatment, and the net economic benefits of the ecosystem increased by 7.1% and 17.1%, respectively. In summary, applying fertilizer at a depth of 25 cm can significantly reduce the environmental footprints and increase maize productivity, making it an effective fertilization strategy in the Loess Plateau region of China.