Calcium carbonate (CaCO3) whisker, as a new type of microfibrous material, has been extensively used in the reinforcement of cementitious materials. However, the combined effect of CaCO3 whisker and fly ash on mechanical properties of cementitious materials under high temperatures was still unknown. In this study, the coupling effect of CaCO3 whisker, and fly ash on mechanical properties of the cement was investigated. Two sets of cement mortars were fabricated, including CaCO3 whisker-based mortar which contained 0 wt.%, 5 wt.%, 10 wt.%, 15 wt.%, and 20 wt.% CaCO3 whisker as cement substitution and CaCO3 whisker-based fly ash mortar which contained 30 wt.% fly ash in addition to 0 wt.%, 5 wt.%, 10 wt.%, 15 wt.%, and 20 wt.% CaCO3 whisker as cement substitution. Mass loss, compressive strength, and flexural strength of these two sets of specimens before and after being subjected to high temperatures of 200°C, 400°C, 600°C, 800°C, and 1000°C were measured. Based on the results of the aforementioned tests, load-deflection test was performed on the specimen which exhibited the superior performance to further study its mechanical behavior after exposure to high temperatures. Moreover, microstructural analysis, such as mercury intrusion porosimetry (MIP) and scanning electron microscopy (SEM), was conducted to reveal the damage mechanism of high temperature and to illustrate the combined effect of CaCO3 whisker and fly ash on high-temperature resistance of the cement. Results showed that fly ash could improve the high-temperature performance of CaCO3 whisker-based mortar before 600°C and limit the loss of strength after 600°C.