To investigate the effect of yeasts on Kazak cheese quality and flavor, three isolated yeasts (Kluyveromyces marxianus A2, Pichia kudriavzevii A11, and Pichia fermentans A19) were used to ferment cheeses and designated as StC, LhC, and WcC, respectively. The cheese fermented with a commercial lactic acid starter without adding yeast was used as control named LrC. The results showed that the texture of cheese added with yeasts were more brittle. K. marxianus A2 contributed to the formation of free amino acids and organic acids, especially glutamate and lactic acid. Moreover, K. marxianus A2 provides cheese with onion, oily, and floral aromas. Furthermore, P. kudriavzevii A11 promotes a strong brandy, herbaceous, and onion flavor. Although no significant aroma change was observed in PfC, it promoted the production of acetic acid, isoamyl acetate, and phenethyl acetate. These results indicate that yeasts are important auxiliary starters for cheese production.