This study investigates the changes of the physicochemical characteristics and flavor of fermented Suanyu (Chinese fermented fish) during fermentation with Lactiplantibacillus plantarum (L. plantarum) and Saccharomyces cerevisiae (S. cerevisiae). The related indicators, including pH, water activity (Aw), volatile base nitrogen (TVB-N), thiobarbituric acid (TBA), free amino acids (FAAs), microbial community, and volatile compounds were determined. L. plantarum fermentation samples (LP) and natural fermentation samples (NF) were used as controls. The pH and Aw of three groups of Suanyu samples decreased continuously through the entire fermentation process. Meanwhile, the TVB-N of three groups of samples increased gradually, while TBA first increased and then decreased. Notably, the pH, Aw, TVB-N, and TBA of MF group samples (inoculated L. plantarum and S. cerevisiae) were significantly lower than the NF group samples. In addition, both TVB-N and TBA of the MF group samples were lower than those of the LP group samples during fermentation, suggesting that combined fermentation could inhibit the growth of undesirable microorganisms more effectively. Lactobacillus were the main bacterial genus of the three group fermented samples during fermentation, and combined fermentation could promote the growth of Lactobacillus more significantly. In addition, the highest content of umami (145.16 mg/100 g), sweet amino acids (405.75 mg/100 g), and volatile compounds (especially alcohols and esters) were found in MF group samples, followed by the NF and LP group samples, indicating that combined fermentation could give Suanyu a better flavor quality. This study may provide a theoretical basis for the industrial production of fermented fish products and the improvement of fermentation technology.