Fermented foods are a potential source to produce novel dipeptidyl peptidase-IV inhibitory peptides (D4IPs). In this study, the fermented mandarin fish (Chouguiyu) was used to screen D4IPs and their formation mechanism was studied by metagenomics and peptidomics. A total of 400 D4IPs with DPP-IV inhibition structure and high hydrophobicity were identified. The correlation network map showed that Lactococcus, Bacillus, Lysobacter, Pelagivirga, Kocuria, Escherichia, Streptococcus, and Peptostreptococcus were significantly correlated with the most D4IPs. Four stable D4IPs, including KAGARALTDAETAT, GEKVDFDDIQK, VVDADEMYLKGK, and GQKDSYVGDEAQ were respectively from the precursor proteins parvalbumin, troponin, myosin, and actin, and were mainly formed by the hydrolysis of subtilisin (EC 3.4.21.62), aspartic proteinase (EC 3.4.23.1), thermolysin (EC 3.4.24.27), oligopeptidase B (EC 3.4.21.83), and proteinase P1 (EC 3.4.21.96) from Bacillus, Kocuria, Lysobacter, Lactococcus, and Peptostreptococcus. The inhibition mainly resulted from the hydrogen bond and salt bridge between D4IPs and DPP-IV enzyme. This study provides important information on the proteases and related microbial strains to directionally prepare D4IPs in Chouguiyu.