Clay is an abundant material worldwide, but due to the high demand for pure kaolinite clay, research into the application of low-grade metakaolin (MK) is required. However, research on the effect of low-grade MK on the volume stability of concrete is lacking. In this work, concrete composed of low-grade MK, replacing 20%–60 % of Portland cement, is studied using nanoindentation, thermogravimetric, creep and strength measurement in order to demonstrate the impact of high-volume metakaolin on the long-term volume stability of concrete materials. Results show that although the incorporation of high-volume MK degrades the early-age mechanical properties of concrete (7–28 d), the addition of an appropriate amount of MK (20 %) improves the long-term compressive strength of concrete (60–180 d). Meanwhile, concrete mixed with MK (~60 %) shows lower creep stress than plain specimen, and the specimen mixed with 20 % MK has the lowest creep stress. From a nanoscale perspective, incorporating an appropriate amount of MK increases the content of high-density calcium silicate hydrate (C–S–H), which provides a positive effect on reducing the creep stress of concrete. For the 20 % MK-modified specimen, the volume fraction of C–S–H increases by 4.23 % compared to the reference sample, and the relative volume fraction of high-density C–S–H increases by 146.77 %. Meanwhile, the contents of pore and Ca(OH)2 phase, as well as the widths of interfacial transition zone (ITZ), are decreased in the 20 % MK-modified samples compared to plain concrete. The results of thermogravimetric analysis also show that the content of Ca(OH)2 decreases with the increase in MK substitution level, and the non-evaporable water content of the 20 % MK-modified paste is similar to that of plain paste. This study provides theoretical guidance for the application of low-grade clay minerals in concrete.