This study investigates the impact of the long-term pozzolanic properties of halloysite nanotube (HNT) on the physical and mechanical properties, permeability, durability, and microstructural characteristics of cement mortar subjected to repeated freeze-thaw cycles. For this purpose, the two-year cured samples were exposed to 300 freeze-thaw cycles. Deterioration of the cement mortar surface was visually assessed and regularly quantified by mass loss and length change. Furthermore, helium porosity, electrical resistivity, and ultrasonic pulse velocity (UPV) were performed on cement mortar mixtures to elucidate the effect of repeated freeze-thaw cycles on permeability. In terms of mechanical properties, compressive and flexural strength tests were conducted; static elastic modulus and flexural toughness were also calculated. The frost durability of samples was analyzed using the relative dynamic modulus of elasticity and durability factor as the indexes to assess mortar's freeze-thaw resistance. Moreover, the microstructures of specimens before and after 300 freeze-thaw cycles were analyzed by scanning electron microscopy. Visual comparisons and experimental results demonstrated that the HNT introduction in cement mortars markedly enhances the frost resistance of plain mortar. It leads to the refinement of the cement paste pore structure and a reduction in its porosity due to the nucleating, filling, and long-term pozzolanic effects of HNT. It was found that the contribution of HNT's pozzolanic activity is the most important of these mechanisms. Therefore, less water penetration into the hardened cement composites occurs, which results in higher frost durability. The samples containing 2 wt.% HNT (by weight of cement) exhibited the lowest mass loss, expansion, porosity, and UPV loss due to repeated freeze-thaw cycles. The highest electrical resistivity and residual mechanical strengths also pertained to samples with 2 wt.% HNT. Hence, the HNT replacement dosage of 2 wt.% can be regarded as an optimal content for the cement mortars studied in this work. Finally, the two-way ANOVA revealed that HNT percentage is the factor with the greatest impact on mass loss, electrical resistivity, and compressive strength. In terms of length change, porosity, and flexural strength, the freeze-thaw cycle was the most statistically important factor.