This study examines the improvement of nano-metakaolin (NMK) on the chloride ion diffusion resistance (CDR) of fly ash (FA) cement-based materials. The rapid chloride diffusion (RCM) method was employed to compare the effects of nano Al2O3, nano CaCO3, nano SiO2, nano attapulgite clay, and NMK on the CDR of cement mortar, and a suitable nanomaterial was identified. Subsequently, the influence of NMK on the CDR, flexural and compressive strengths of FA cement mortar was examined. The chloride ion concentration of NMK/FA cement paste under simulated salt environment were measured. The action mechanism of NMK on the CDR of FA cement mortar was explored through mercury intrusion porosimetry and scanning electron microscopy tests. The results reveal that among these nanomaterials, NMK exhibited the highest cost-effectiveness in enhancing CDR of cement mortar, with a suitable content of 5 wt%. NMK demonstrated a significant improvement in the CDR of FA cement mortar, particularly at a hydration age of 7d. Incorporating 5 wt% NMK into the cement mortar with addition of 30 wt% FA resulted in a 73% reduction in chloride ion diffusion coefficient (Dcl) compared to the cement mortar with the addition of 30 wt% FA at 7d. NMK enhances both flexural and compressive strengths of FA cement mortar at various hydration ages (3, 7, 14, 28 d). The addition of 5 wt% NMK makes a increment of about 10% for the flexural strength of cement mortar with 30 wt% FA at 7d. Moreover, NMK results in a denser internal structure of FA cement mortar, facilitates the generation of C–S–H gel, and reduces the more-harmful pores and harmful pores while increasing harmless and of less-harmful pores cement paste. Additionally, NMK exhibited the most substantial reduction in chloride ion concentration within FA cement paste at 7d. In general, NMK significantly enhances CDR, flexural and compressive strengths of FA cement mortar, especially at a hydration age of 7d.