To replace traditional pool and jar fermentation methods, an in-bag fermentation process for mustard greens was investigated. Small-leaf mustard greens were inoculated with 1.0% compound lactic acid bacteria (LAB) (Lactiplantibacillus plantarum: Pediococcus acidilactici=2:1) and subjected to in-bag fermentation. Blanching conditions were optimized, and changes in sensory quality, physicochemical indices, and microbial characteristics during fermentation were systematically evaluated. Microbial community structures were analyzed using 16S rDNA and ITS high-throughput sequencing. The results showed that blanching in boiling water (100 ℃) for 1 min provided optimal microbial control and sensory quality. During the 20-day fermentation period, pH decreased from 5.78 to 3.21, total acidity increased from 0.48 g•L-1 to 6.13 g•L-1, and nitrite content remained consistently below 1.46 mg•kg-1. The highest sensory score (36.30) was observed on day 15. LAB and total bacterial counts rapidly increased to 4.33×108 CFU/mL and 4.47×108 CFU/mL, respectively, within the first 0~5 days, followed by a decline to 7.07×106 CFU/mL and 9.23×106 CFU/mL, respectively, and stabilization after day 15. Yeast and mold counts increased during the first 10 days, reaching a maximum of 4.40×106 CFU/mL on day 10, and then remained stable. Coliform bacteria were undetectable after 5 days of fermentation. High-throughput sequencing revealed a relatively simple microbial community structure, with L. plantarum (83.15%) and P. acidilactici (16.10%) as the dominant bacterial species, and Meyerozyma guilliermondii (66.46%) and Hanseniaspora meyeri (30.81%) as the dominant fungal species. These results demonstrate that in-bag fermentation is a safe and feasible approach for mustard greens and provides a promising alternative for overcoming production bottlenecks in fermented vegetable processing.