Abstract: In recent years, continuous pepper cropping and unreasonable application of high nitrogen (N) fertilizer have been the main factors inhibting pepper cultivation with high yield and quality. At present, many theories attempt to explain the interspecific competition in intercropping systems. Moreover, arbuscular mycorrhizal fungi (AMF) in soil has attracted increasing attention from scientists to improve interspecific competitive interactions. AMF can promote plant nutrient absorption, growth, and development. However, there are few systematic reports on the relationship between AMF on plant interspecific competition and its response to N fertilizer. Therefore, this study aimed to explore the effects of AMF on plant growth, interspecific complementarity, and nutrient competition in an intercropping system of pepper and common bean under different organic N application levels. This can lay down the foundation for diversified planting of protected vegetables and efficient utilization of nutrient resources. Pot experiments were conducted for three different planting modes: pepper-common bean intercropping, pepper monoculture, and common bean monoculture; and two native AMF treatments: without indigenous AMF (NM) and indigenous AMF inoculation (AMF); and two N treatments: no N (N0), organic N (glutamine, 120 mg·kg⁻¹, N120). The effects of inoculation of indigenous AMF, application of organic N and intercropping on plant growth, and interspecific competitiveness of pepper and common bean were studied. The results showed that the inoculation of indigenous AMF infected both common bean and pepper, and organic N application showed the promoting effects. Compared with NM, AMF inoculation significantly increased the aboveground biomasses, plant height of pepper and common bean. The N absorption efficiencies were also increased by 108% under N0 treatment and 98% under N120 treatment for intercropping common bean, and by 40% under N0 treatment and 22% under N120 treatment for intercropping pepper. The results showed that the response of N absorption efficiency to the planting mode was in the order of common bean > pepper, and the N absorption competition of common bean was stronger than that of pepper. Under NM conditions, the competitiveness of pepper to resources was stronger than that of common bean, the interspecific competitiveness of pepper relative to the common bean was 0.60, and pepper was in a dominant position. Under AMF conditions, the competitiveness of pepper to resources was lower than that of common bean, the interspecific competitiveness of pepper relative to the common bean was −0.37, and pepper was at a disadvantage position. Both were more obvious under the N120 condition and significantly increased by 125% and decreased by 19% compared with N0, respectively. It can be seen that the interspecific competitiveness of pepper and common bean was different under different treatments. In all composite treatments, inoculation of indigenous AMF and application of a certain amount of organic N can significantly promote the growth of pepper and common bean, and can also significantly change the interspecific competitiveness of pepper relative to common bean.