Maize/soybean intercropping systems improve resource use efficiency through interspecific complementarity. However, the regulatory mechanisms by which the partial replacement of chemical nitrogen fertilizer by organic fertilizer and biofertilizer affects crop growth and productivity in maize/soybean systems remain unclear. A two-year field experiment (2024–2025) was conducted in the Hexi oasis irrigation district of Zhangye, Northwest China. The main plots were assigned to fertilization regimes (conventional nitrogen, N1; reduced nitrogen, N2; organic substitution, ON2; and biofertilizer substitution, BN2), and the subplots were assigned to cropping systems (maize monoculture, soybean monoculture, and maize/soybean intercropping). A logistic growth model was used to simulate dry matter accumulation, and the land equivalent ratio (LER), net effect (NE), complementarity effect (CE), and selection effect (SE) were employed to evaluate intercropping advantage. Mantel analysis was applied to analyze relationships between crop growth parameters and system grain yield. Study results showed that cropping system fertilization regime, year, and their multiple interactions had significant effects on maize, soybean, and system grain yields (p < 0.001). Under all fertilization treatments, the LER of the maize/soybean intercropping system was greater than 1, indicating that intercropping had higher land-use efficiency than monoculture. Compared to the weighted mean of monocultures, ON2 enhanced intercropping grain yield by 25.30% over two years driven primarily by positive SE. Compared to conventional N practice, ON2 increased intercropped maize grain yield by 19.98% and 12.40% in 2024 and 2025, respectively, while BN2 enhanced intercropped soybean yield by 22.60% in 2025. Together, system grain yield followed the rank ON2 > BN2 > N1 > N2. Mantel tests further revealed that maize maximum biomass potential (Ymax) was highly significantly and positively correlated with system grain yield (p < 0.01), and maximum growth rate (Imax) was significantly positively correlated (p < 0.05), whereas soybean growth parameters showed no significant correlation with system yield. Overall, partial substitution of chemical fertilizer with organic fertilizer enhances maize biomass accumulation and fosters positive interspecific interactions, thereby increasing grain yield in maize/soybean intercropping. These findings provide a practical basis for reducing chemical fertilizer use while maintaining productive and sustainable cropping systems.