Inoculation of starter culture is a viable method to improve the quality of fermented foods, but its effect on the flavor metabolite profiles and the underlying mechanisms are still unclear. This study aimed to elucidate the effects of starters (Lactiplantibacillus plantarum (LP) and Staphylococcus simulans (SS) individually or in combination (LS)) on the flavor metabolite profiles of fermented sausages via metabolomics and genomics. L. plantarum markedly modified the composition of bacterial communities and made Lactobacillus spp. dominant in sausages (98.29% and 85.03% in LP and LS groups, respectively). Additionally, inoculation with a single starter, L. plantarum, and a mixed starter yielded similar non-volatile flavor metabolites, which were mainly characterized at the amino acid and peptide levels (relative intensities of 349.65 and 348.62 for the LP and LS groups, respectively). Meanwhile, the mixed starter group had the most volatile flavor metabolites (relative intensity of 34728.67), some of which were contributed by L. plantarum, such as ethyl acetate (relative intensities of 583.33 and 588.33 for the LP and LS groups, respectively) and benzaldehyde (relative intensities of 786.67 and 909.00 for the LP and LS groups, respectively), and several of which were generated by S. simulans, such as ethyl propionate (relative intensities of 214.67 and 136.67 for the SS and LS groups, respectively) and benzyl alcohol (relative intensities of 720.00 and 656.00 for the SS and LS groups, respectively). Furthermore, L. plantarum was found to possess more genes encoding peptidases (48) and carbohydrate-active enzymes (124), while S. simulans had more genes related to lipid hydrolysis (12). In conclusion, differences in the properties and combinations of indigenous strains play a crucial role in the generation of flavor metabolites in sausages.