Accurate evaluation of pore systems in shale reservoirs is critical for understanding fluid flow, gas storage capacity, and overall reservoir performance. Extensive research has been conducted on the micro- and nano-pore structure of shale reservoirs using various experimental methods and shale samples. However, discrepancies in sample preparation standards and experimental parameters—such as observation techniques and data interpretation—raise concerns about the reliability and comparability of these results across different shale reservoirs. This review systematically evaluates the current methods for characterizing shale pore systems, with particular emphasis on commonly used techniques such as scanning electron microscopy (SEM), gas adsorption, and CT scanning. Key challenges related to sample preparation (e.g., sample size) and experimental conditions (e.g., voltage and current) are discussed, as these factors can introduce significant inaccuracies into pore structure characterization, even for well-established methods. Additionally, we examine the difficulties in integrating these methods to achieve a comprehensive understanding of shale pore parameters, including the quantification of organic and inorganic porosity, full-scale pore size distribution, and pore connectivity. Addressing these challenges requires the establishment of standardized processing workflows to enhance the comparability of results and minimize experimental errors. We also highlight often-overlooked issues, such as the potential discrepancy between pore structures observed under laboratory conditions and those at in-situ depths. The review concludes with recommendations for future research, including the development of advanced experimental techniques and more efficient data processing strategies to improve pore characterization in shale reservoirs. This review provides a new perspective for future research and addresses a critical gap in understanding the impact of experimental conditions on pore structure characterization outcomes.