This paper takes the cement clay of different cement contents as the studied object. The samples of cement clay soil are used for nuclear magnetic resonance test to study the effect of cement content on the distribution of micro-pore. The samples are used for the variable water head penetration test to study the effect of cement content on permeability. On this basis, the paper investigates the microscopic mechanism of the effect of cement content on permeability. The study results show the follow. The permeability coefficient of cement-soil decreases as the cement content increases. It decreases intensely at cement content ranging from 4%to 12%, and decreases slowly at cement content ranging from 15%to 25%. There are three peaks in the T2 distribution curves of cement-soil, which correspond to small pores, medium pores and large pores, respectively. As the cement content increases, the total area of T2 distribution curve tends to decrease. At the stage of low cement content, the area of the second and third peaks diminishes obviously. But at the stage of high cement content, the area of the first peak diminishes obviously. Thus it can be seen that in the range of low cement content, the hydration of cement-soil is prior to block up large pores and medium pores, which makes the permeability coefficient decreases significantly with the increase of cement content. While in the range of high cement content, the area of small pores mainly declines with the increment of cement content. But that of large pores and medium pores has little difference, so the increase of cement content has little effect on the decrease of permeability coefficient of cement-soil.