Mongolian cheese is non-fermented cheese, which easily deteriorates during storage because of hydrolysis. The freezing points of sucrose and sucrose-free cheese were measured −5.16 °C and −4.29 °C, respectively. Ice-storage temperatures of −2 °C and −4 °C were used and 0 °C was used as reference temperature. In this study, the changes of proteolytic indexes (PI) and total viable counts (TVC) of cheese at different ice-temperatures during storage were studied. The PIs of all treatments increased over storage time, which conformed to the Arrhenius first-order kinetic model. The shelf lives of sucrose and sucrose-free cheese were predicted. In addition, −4 °C effectively suppressed the increases in TVC and PIs. The split-split-plot design was applied in comparing the effects of cheese type, the storage time and storage temperature on PI. Storage time was the most important factor followed by cheese type and storage temperature.