Choosing a good crop rotation plan helps maintain soil fertility and creates a healthy soil ecosystem. However, excessive fertilization and continuous cultivation of vegetables in a greenhouse results in secondary salinization of the soil. It remains unclear how crop rotation affects Yunnan's main place for vegetable growing in the greenhouse. Six plant cultivation patterns were chosen to determine how different rotation patterns affect the chemical properties and the soil microbial communities with secondary salinization, including lettuce monoculture, lettuce-large leaf mustard, lettuce-red leaf beet, lettuce-cabbage, lettuce-romaine lettuce, and lettuce-cilantro (DZ, A1, A2, A3, A4, and A5). The results showed that all treatments increased the proportion of nutrients available in the soil, and the effect of the A1 treatment was the most significant compared to the monoculture mode. The high-throughput sequencing findings revealed that distinct crop rotation patterns exerted varying effects on the microbial communities. Microbial community diversity was significantly lower in the monoculture than in the other treatments. The number of microbial operational taxonomic units OTUs was significantly higher in the crop rotation modes (P < 0.05), and the A1 treatment had larger numbers and diversity of bacterial and fungal OTUs (Shannon's and Simpson's) than other treatments (P < 0.05). Prominent bacterial and fungal communities were readily observable in the soils planted with rotational crops. Proteobacteria had the highest relative abundance of bacteria, whereas Ascomycota was the most abundant fungus. The principal coordinate analysis at the OTU level separated soil bacterial and fungal growth communities under the different treatments. Among the six treatments, The first two axes (PC1 and PC2) described 46.44 % and 42.42 % of the bacterial and fungal communities, respectively. Network-based analysis showed that Bacteroidota and Gemmatimonadota members of the genus Bacteroidota were positively correlated with Proteobacteria. Members of Ascomycota and Chytridiomycota exhibited positive relationships. These results extend the theoretical understanding of how various crop rotation patterns affect soil chemical properties, microbial community diversity, and metabolic functions. They reveal the beneficial effects of crop rotation patterns on enhanced soil quality. This study provides theoretical guidance for the future enhancement of sustainable agriculture and soil management planning.