The naturally fermented Inner Mongolian cheese’s flavor and nutritional value make it a popular choice among customers. In this work, to create multi-functional peptides that have taste and biological activity, peptidomics and bioinformatics were used to screen flavor peptides from Inner Mongolian cheese and further assess their antioxidant and angiotensin I-converting enzyme (ACE) inhibitory properties. According to sensory data, YH8 and IL7 had detectable bitter tastes with low thresholds of 0.03 and 0.06 mmol/L, respectively. With an umami threshold range of 0.24‒0.81 mmol/L, VQ6, FK13, HP13 and QT14 exhibited a range of flavors dominated by umami, including sweet, bitter, salty, sour and kokumi. Antioxidant activitywise, YH8, VQ6, HP13 and QT14 were well represented. The above-mentioned peptides all had some ACE inhibitory effect. The bitter peptide IL7 (IC50 = 0.09 mmol/L) had the highest level of ACE inhibitory activity, followed by YH8 (IC50 = 0.33 mmol/L). These multi-functional peptides, which have been assessed for bioactive and taste features in Inner Mongolian cheese, may have positive impacts on health and harmonize the cheese’s overall flavor. These results suggest that some flavor peptides produced in fermented foods might be with bioactivities while providing a basis for the exploration and application of multi-functional peptides.