Natural hydraulic lime mortar plays an important role in cultural heritage conservation but its low early strength and slow hydration rate limit its application in modern heritage restoration projects. In this study, nano-metakaolin (NMK) was added into natural hydraulic lime (NHL2) to improve its early performance further, and mechanical experiments, workability experiments, water resistance experiments, dry-wet cycling experiments, and freeze-thaw experiments were used to comprehensively evaluate the applicability of the modified material for cultural heritage protection. X-ray diffraction (XRD), thermogravimetry Analysis (TG), mercury intrusion porosimetry (MIP), scanning electron microscopy (SEM), and other microscopic methods were used to analyze and characterize the enhancement mechanism. The results show that low doping of NMK significantly improves the early mechanical properties of NHL2. The content of 6% NMK can increase the compressive strength (3d,7d,28d) of NHL2 by 188.1%,317.4%,314.3%, and the flexural strength by 79.4%,177.6%, and 96.9%, while, the fluidity of NHL2 decreases by only 6.6%; In terms of water resistance, NMK has little effect on the softening coefficient and saturated water absorption, and 6% NMK only increased the softening coefficient of NHL2 by 3.2% and decreased the saturated water absorption by 0.30%. In terms of durability, under salt solution erosion and dry-wet environments, the addition of NMK significantly enhances the corrosion resistance of NHL2 under dry-wet cycling conditions of sulfate solution, and the corrosion resistance increases and then decreases with the increase of NMK dosage. In the freeze-thaw environment, the addition of NMK also improves the frost resistance of NHL2 and delays the rupture of the test piece caused by the freezing and expansion of internal water. The NHL2 with 6% NMK dosage shows the best performance in terms of corrosion resistance and freezing resistance compared with the rest of the group. Microscopic characterization shows that NMK promotes the early hydration reaction of NHL2, which leads to an increase in the hydration product calcium-silicate-hydrate (C-S-H), and its needle-like and reticular structure connects all the materials to form a dense structure, which improves the early strength of NHL2. In the late stage of hydration, NMK accelerates the carbonation, resulting in the decrease of calcium hydroxide (Ca(OH)2) and the increase of calcium carbonate (CaCO3); Furthermore, NMK pushes the average pore size and the most available pore size of the internal pores of NHL2 to decrease, resulting in a more pronounced strength rise in the later stages. In conclusion, NMK, as an inexpensive and abundant nanomaterial, has a superior potential in the restoration of geotechnical artifacts, and ancient buildings.