To explore the effects of fermentation methods on the microbial communities and metabolites in dry fermented mutton sausages, the differences in the microbial communities and metabolites in naturally fermented and starter culture-fermented mutton sausages were analyzed by high-throughput sequencing and metabolomics, and the correlation between microbial communities and significantly differential metabolites (SDM) was investigated. The results showed that inoculated fermentation had obvious effect on the microbial community of mutton sausages. At the genus level, Leuconostoc, Rahnella, Brochothrix and Debaryomyces were dominant during natural fermentation, and Leuconostoc, Brochothrix, Psychrobacter, Pediococcus, Debaryomyces and Penicillium were dominant during inoculated fermentation. Inoculate fermentation increased the types and contents of flavor substances, especially esters and amino acids. Based on multivariate statistical analysis, 29 volatile metabolites and 16 non-volatile metabolites that significantly differed between the natural and inoculated fermentation groups were identified (fold change (FC) > 2, variable importance in the projection (VIP) > 1, P < 0.05). Besides, correlation analysis showed that seven bacterial genera (Leuconostoc, Brochothrix, Pediococcus, Psychrobacter, Enterococcus, Rahnella and Staphylococcus) and seven fungal genera (Debaryomyces, Penicillium, Aspergillus, unspecified_Aspergillaceae, unspecified_Capnodiales, unspecified_Capnodiales, Rhizopus and unspecified_Basidiomycota) were regarded as core microorganisms (| r | > 0.8, P < 0.05).