The presence of abundant clay components and microporous structure in shale results in its high hydrophilicity, making a water-rich environment inevitable in petroleum exploration projects. Therefore, it is crucial to consider the influence of bedding structure, moisture content, confining pressure, and their combined effects on the geomechanical properties of shale. This article aims to investigate the mechanical properties of deep shale under varying water content conditions, elucidate the failure mode and failure mechanism of shale in actual engineering scenarios, and explores the interplay between stress, structure, moisture content, and other factors on its mechanical properties. The evaluation of wellbore stability and fracture propagation effects is proposed based on laboratory experiments using triaxial stress and strain data, along with the application of energy evolution theory. The experimental procedures encompass an analysis of shale's microscopic components and structure, as well as anisotropic shale triaxial compression tests conducted under different moisture contents and confining pressures. The results demonstrate that shale exhibits dense pores in its microstructure and displays pronounced anisotropic characteristics in its macrostructure. The presence of water within these pores, combined with the in situ stress within the formation, significantly influences the mechanical properties of shale. This anisotropy decreases with increasing moisture content, but the mechanical performance still decreases. Under triaxial compression conditions, the increase in confining pressure to some extent enhances the anisotropy of shale's deformation characteristics, which is related to the failure modes of shale. However, the detrimental effect of moisture content on shale's mechanical properties still persists. In order to quantify the impact of these factors, this study utilizes the elastic modulus as an indicator of the coupling effect. It combines the triaxial strain curve obtained from laboratory tests and proposes an evaluation index for shale mechanical properties based on the energy evolution theory. This index is suitable for assessing wellbore stability (the stability index called SIr) and crack expansion (the brittleness index called BIr). The calculation results reveal that, during the wellbore drilling process, excavating parallel to the direction of shale bedding while maintaining low moisture content and high confining pressure yields a higher SIr value, indicating better wellbore stability. On the other hand, during reservoir fracturing, fracturing perpendicular to the shale bedding direction and maintaining low confining pressure and moisture content result in a smaller BIr value. This approach is more beneficial for the expansion of shale fracture network in engineering.