Abstract: To address the severe problem of continuous cropping obstacles in facility vegetables and clarify the impact of different rotation patterns on the soil microorganisms in facilities, based on the metagenomic sequencing technology, this study investigated the microbial community structure and diversity, interaction networks, and community functional changes under three rotation patterns: lettuce-rice (H), lettuce-upland rice (S1), and lettuce-looseleaf lettuce (S2).The results indicated that compared with continuous lettuce cultivation (CK), all three rotation patterns increased the α-diversity of soil bacterial communities to varying degrees. Under the lettuce-rice rotation pattern, the Chao1 and ACE indices increased most significantly, and the Simpson index decreased significantly. The Shannon index increased most significantly under the lettuce-rye rotation pattern. PCoA analysis and PERMANOVA analysis showed that the three rotation patterns significantly changed the composition of soil bacterial communities. The four genera, Bradyrhizobium, Gp6-AA40, PSRF01, and VBCG01, were significantly enriched under all three rotation patterns, and the relative abundance of Bradyrhizobium and PSRF01 was the highest under the lettuce-rice rotation treatment. The co-occurrence network analysis indicated that crop rotation enhanced the complexity and stability of the microbial network, and altered keystone taxa. The key functional microorganisms included beneficial bacteria such as PSRF01, Bradyrhizobium, Nitrospira, Sphingomicrobium, and Lysobacter. Based on the prediction of microbial function of KEGG, it was found that the relative abundance of 17 subfunctional genes was significantly enriched under the three crop rotation treatments. Among them, the abundance of 12 functional genes, including membrane transport, transport and catabolism, environmental adaptation, carbohydrate metabolism, and energy metabolism, increased most significantly in the lettuce-rice rotation mode. To sum up, the three different rotation patterns have significantly changed the composition, diversity and function of microbial community in protected soil. Among them, the paddy upland rotation pattern (lettuce-rice) has the best performance in all aspects. Therefore, the ideal rotation pattern to alleviate or avoid the obstacle of protected lettuce continuous cropping is rice lettuce rotation, followed by upland rice lettuce rotation.