The clay of the strata along shallow-buried tunnels of Hefei Rail Transit Line 1-5 mainly consists of Holocene clay and Late Pleistocene clay, which can be called neo-clay and old clay respectively according to their formation age. The engineering characteristics of the two kinds of clay are different mainly in that the neo- clay is expansive while the old clay is not. In order to better understand the causes for the differences between the two clays, the physical and mechanical parameters of these two kinds of clays were analyzed on the basis of data from the geological examination along Hefei Rail Transit Line 1-5, and preliminary conclusions of the dif- ferences between the two kinds of clay were made. Besides, the correlation between the physical and mechanical parameters of the two kinds of clay was explored. This paper also studied the characteristics of both clay and their existing variances through the lens of microscope, explained the influence of microstructure of the two kinds of clay on their engineering properties. It concluded that the obvious differences in physical indexes such as hy- drophily, compressibility and shear strength between neo-clay and old clay in Hefei area, and the differences of their variant microstructures led to their different soil engineering characteristics.