Acid contamination has a notable influence on the geotechnical properties of soil and this influence is strongly dependent on contamination concentration (pH) and contamination duration. To fully investigate the effect of acid contamination on the microscopic and strength properties of natural clay, a series of micro- and macrolaboratory tests were performed in this study, and the mechanism of this effect was comprehensively revealed. Microscopic analysis indicates that acid contamination could lead to some mineral transformations in clay, such as illite-smectite transforming into chlorite and illite transforming into kaolinite. Besides, more large pores and a looser structure can be observed in the clay due to the erosional effects of acid contamination, which could effectively weaken the strength properties of natural clay. The experimental results also indicated that, when subjected to acid contamination, the lower contamination pH could lead to a notable decrease in clay's shear strength, while the clay's shear strength increased initially and then decreased as contamination duration increased. In addition, gray correlation analysis results demonstrated that calcite has a significant effect on cohesion, while also indicating a strong correlation between illite and the internal friction angle.