The dams, foundation pit support and anti-fouling works of water conservancy projects are all related to permeability of soil. It is necessary to calculate the permeability coefficient of soil accurately for civil engineering and practical water conservancy projects. Though relevant scholars have carried on plenty of research on theories and experiments of permeability coefficient of clay, there are certain errors between the calculation results of traditional empirical formula of permeability coefficient and the measured data of permeability test. This has a great impact on the reinforcement and restoration of practical engineering construction. In this paper, two types of clay are selected to make samples, which combine with experiments on permeability coefficient of variable sources to study the effect on void ratio of clay on permeability coefficient and fit the functional relation between void ratio of clay and permeability coefficient. Furthermore, the reasons for distinct errors in calculating clay by traditional empirical formula of permeability coefficient are discussed. The research achievement accords with the rule of clay permeability, providing a reference for engineering seepage control and foundation settlement.