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The intercropping of nitrogen-fixing and non-nitrogen-fixing tree species changed the availability of soil nitrogen and soil microbial community structure and then affected the regulation process of soil carbon and nitrogen cycle by microorganisms in an artificial forest. However, there is no consensus on the effect of soil nitrogen on soil microorganisms. In this study, the intercropping of mulberry and twigs was completed through pot experiments. Total carbon, total nitrogen, and total phosphorus in the rhizosphere soil were determined, and the composition and structure of the soil microbial community were visualized by PCR amplification and 16S rRNA ITS sequencing. The analysis found that the intercropping of <i>Morus alba</i> L. and <i>Lespedeza bicolor</i> Turcz. had no significant effect on soil pH but significantly increased the contents of total carbon, total nitrogen, and total phosphorus in the soil. The effect on the alpha diversity of the bacterial community was not significant, but the effect on the evenness and diversity of the fungal community was significant (<i>p</i> < 0.05). It was also found that soil nutrients had no significant effect on bacterial community composition but had a significant effect on the diversity within the fungal community. This study added theoretical support for the effects of intercropping between non-nitrogen-fixing tree species and nitrogen-fixing tree species on soil nutrients and microbial community diversity.