A sustainable model of combined organic–inorganic fertilizer application for high maize yields and environmental health is important for food security. The short-term combined application of organic and inorganic fertilizers can improve crop yields; however, the effect of different proportions of organic and inorganic fertilizers on the maize yield and nitrogen gas emissions in a long time series has not been reported. In this study, field experiments and DeNitrification-DeComposition (DNDC) model simulations were used to study the long-term effects of substituting inorganic fertilizers with organic fertilizers on crop yields and nitrogen-containing gas emissions. Six treatments were included: no nitrogen (CK); urea (U1); and 25%, 50%, 75%, and 100% of the urea N substituted by organic fertilizers (U3O1, U1O1, U1O3, and O1, respectively). The DNDC model was calibrated using the field data from the U1 treatment from 2018 to 2020 and was validated for the other treatments. The results showed that this model could effectively simulate crop yields (e.g., nRMSE < 5%), soil NH3 volatilization, and N2O emissions (nRMSE < 25%). In addition, long-term (26 years) simulation studies found that the U1O1 treatment could considerably increase maize yields and ensure yield stability, which was 15.69–55.31% higher than that of the U1 treatment. The N2O, NH3, and NO emissions were in the descending order of U1 > U3O1 > O1 > U1O3 > U1O1, and the total nitrogen-containing gas emissions from the U1O1 treatment decreased by 53.72% compared with the U1 treatment (26 years). Overall, substituting 50% of inorganic nitrogen with organic nitrogen could maintain the high yield of maize and reduce emissions of nitrogen-containing gases, constituting a good mode for the combined application of organic–inorganic nitrogen in this area.
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