The study aimed to thoroughly investigate the effects of nitrogen deposition on the growth, chlorophyll fluorescence and yield of Zanthoxylum bungeanum Maxim. in both monoculture and intercropping systems with Capsicum annuum L. and Glycine max. The research provided a detailed evaluation of how nitrogen deposition influenced soil and plant parameters within these intercropping systems. Key findings include: (i) In the Z. bungeanum monoculture, nitrogen deposition led to a 346.5% increase in soil NO₃⁻ levels, significantly affecting chlorophyll fluorescence parameters and decreasing soil pH. (ii) In the Z. bungeanum–C. annuum intercropping system, nitrogen deposition influenced the growth and chlorophyll fluorescence of both crops and resulted in a 261.5% increase in the root length of C. annuum. (iii) In the Z. bungeanum–G. max system, nitrogen deposition negatively impacted the chlorophyll fluorescence of G. max, reduced Z. bungeanum yields by 89.3% and altered its chlorophyll fluorescence parameters. These changes likely hindered the nitrogen-fixing capacity of G. max due to altered soil conditions. Overall, the Z. bungeanum–C. annuum system showed superior performance by enhancing soil NO₃⁻-N content. In contrast, the Z. bungeanum–G. max system experienced reduced yields due to the adverse effects of nitrogen deposition on symbiotic nitrogen fixation. These findings are crucial for developing agricultural strategies aimed at improving crop adaptability and yield in response to environmental changes.