In this study, diatomite was used in cement mortar to improve the frost resistance durability. Experimental results showed that using diatomite instead of a small amount of silica fume (such as the samples in D-33.3%) can effectively enhance the frost resistance of cement mortar. To comprehensively understand the modification mechanism of diatomite, pore structure of cement mortar considering the effect of freeze-thaw cycles was studied by means of mercury intrusion porosimetry (MIP) and nitrogen adsorption-desorption measurement (NAM). Moreover, cumulative pore volume distribution (CPVD) results had the respective suitable measurement range using MIP and NAM due to the difference of calculation methods. Thus, to obtain more accurate results, the modified CPVD was proposed by the combination of MIP and NAM results. Furthermore, several characteristic pore volumes (including gel pores, transition pores, capillary pores and large pores) were determined according to the mentioned modified CPVD. Finally, multifractal analysis was carried out to explore the pore structure evolution mechanism, where the heterogeneity and connectivity of pore structure inside cement mortar containing diatomite subjected to freeze-thaw cycles were investigated based on the results of modified CPVD.