Abstract: Abstract: Cheese consumption in China has largely increased in recent years. Manual milking manner in small-scale dairy farms may induce the mixing of somatic cells (SCs) into raw milk, which would exert an effect on the final quality of cheese. However, the effect of different SC compositions and related protease activities on cheese quality has not yet been elucidated. In this study, three sources of SCs were recovered and re-introduced into skim milk to ensure the same initial milk quality. SCs A were obtained directly from the udder of healthy cows, and SCs B and C were isolated from milk of healthy cows and cows with mastitis, respectively. Three SCs isolates were then mixed with the skim milk to obtain milks with different SCs compositions for cheese manufacture. Among the three experimental cheeses, the highest epithelial cell count was found in cheese A (65.41%), the highest macrophage and lymphocytes counts was in cheese B (78.15% and 12.15%, respectively), and the highest polymorphonuclear neutrophil count (PMN) was in cheese C (34.23%). The results indicated that there were differences in protease activity and proteolysis level among the cheese samples during ripening. The activity of plasmin and cathepsin B was significantly higher in cheese C than in other cheese samples after 90 d of ripening. In addition, the retention rate of intact αs1-, αs2- and β-CN, and the levels of pH value 4.6 soluble nitrogen and 12% trichloroacetic acid soluble nitrogen were in the order of C