Abstract: Heterogeneity of permeability in fractured media is a hot research topic in hydrogeology. Numerous approaches have been proposed to characterize heterogeneity in the last several decades. However, little attention has been paid to correlate permeability heterogeneity with geological information. In the present study, several causes of permeability heterogeneity, that is, lithology, tectonism, and depth, are identified. The unit absorption values (denoted as ω), which are results obtained from the packer test, are employed to represent permeability. The variability of permeability in sandstone–mudstone is so significant that the value of unit absorptions span 3–4 orders of magnitude at any depth with several test sections. By declustering, it has been found that under a similar tectonic history, the means of permeability differ greatly at different formations as a result of different mudrock contents. It has also been found that in the same formation, permeability can be significantly increased as a result of faulting. The well-known phenomenon, the decrease in permeability with depth, is found to be caused by the fractures in the rock mass, and the relationship between permeability and depth can be established in the form of logω–logd. After subtracting the trend of ω with absolute depth, the mean of the residual value at each relative depth can be well correlated with the distribution of mudstone. The methods proposed in this paper can be utilized to research in similar study areas.