Wettability, as a vital tool for analyzing and describing oil flow, plays a significant role in determining oil/water relative permeability, residual oil distribution, and on–site recovery efficiency. Although the contact angle method is widely used for measuring wetting behavior, it is susceptible to the effects of surface roughness, oil–water saturation, and the distribution of mixed wetting within the range of droplet sizes. Additionally, millimeter–scale droplets fail to accurately represent the wetting distribution and the influencing factors at the micro/nano–scale. Therefore, this study presents a comprehensive investigation of the microstructure and wettability of shale samples. The characterization of the samples was performed using scanning electron microscopy (SEM) and atomic force microscopy (AFM) techniques to gain insights into their microscopic features, surface properties, and wettability. Results demonstrate the following: (1) Quartz and clay minerals tended to exhibit rough surface topography, appearing as darker areas (DA) under scanning electron microscopy (SEM). It is worth noting that plagioclase minerals exhibited brighter areas (BA) under SEM. (2) An increase in the content of minerals such as quartz and clay minerals was observed to decrease the surface oil wetting behavior. In contrast, plagioclase feldspar exhibited an opposite trend. (3) Based on the adhesive forces of the samples towards oil or water, a wetting index, I, was established to evaluate the wettability of shale at a microscale. The dimensionless contact angle W, obtained by normalizing the contact angle measurement, also consistently indicated oil wetting behavior. (4) By comparing the differences between I and W, it was observed that surface roughness significantly affected the behavior of water droplets. The presence of roughness impeded the contact between the solid and liquid phases, thus influencing the accuracy of the wetting results. Organic matter also plays a significant role in influencing surface wettability, and its distribution within the shale samples can lead to localized variations in wettability.