Kaolin is a common clay minerals in nature and a layered aluminosilicate mineral. Small molecule oxalic acid and citric acid were selected as composite organic acids, and kaolin was subjected to acid activation treatment to prepare an organic acid activated metakaolin by high temperature calcination and mechanical grinding. The influences of organic acid activation methods on the microstructure of kaolin were analyzed through SEM and TEM, and the influence of organic acid activated metakaolin on macroscopic properties such as mechanical properties, drying shrinkage performance, electrical flux of concrete and microscopic pore structure was studied, and its microscopic mechanism of action was revealed. The results show that organic acid activation leads to the dissolution of some Si and Al in kaolin, causing damage to the edges and interlayer of the layered structure, resulting in a relatively rough microstructure. The calcination temperature decreases by 160 ℃ and the specific surface area increases. Adding organic acid activated metakaolin to concrete can improve the comprehensive performance of concrete by enhancing the compactness of concrete. The compressive strength at 28 d increases by 23. 2% , and the 28 d electric flux is reduced by 51. 8% , which is superior to metakaolin and silica fume.