Maize/alfalfa intercropping serves as an important practice for enhancing soil functions, with significant potential in improving soil structure and nutrient cycling. However, it is unclear how such intercropping system regulates microbial community structure and interannual dynamic succession in cinnamon soil regions, particularly about the long-term effects of different row ratio configurations. We investigated the effects and interannual stability of different maize/alfalfa row ratio configurations in the cinnamon soil region of northwestern Liaoning. There were five planting treatments in a field experiment, including maize monoculture (SM), alfalfa monoculture (SA), maize-2-rows/alfalfa-2-rows intercropping (M2A2), maize-2-rows/alfalfa-4-rows intercropping (M2A4), and maize-4-rows/alfalfa-4-rows intercropping (M4A4). High-throughput sequencing was employed to analyze soil microbial diversity and community structure. The results showed that maize/alfalfa intercropping significantly increased microbial diversity and altered the community structure of soil fungi, while there was no significant variation in soil bacterial community composition among treatments. The maize/alfalfa intercropping (M2A2 and M4A4) significantly enhanced soil microbial diversity by improving nitrogen availability and other physicochemical properties. In general, this study provides a theoretical basis for optimizing planting patterns to enhance farmland ecological functions in northwestern Liaoning.