Abstract: Microscopic pore structures of shale are the basis for investigating the adsorption and migration mechanism of shale gas and building a geological model. Ar ion milling combined with Scanning Electron Microscopy (SEM) is the main technique for analyzing microscopic pore structures of shale. However, previous research focused mainly on pore classification and lacked insufficient studies on the quantitative characteristics of pore structures. In order to conduct quantitative research on pore structures and improve the quality of pore segmentation, edge detection, watershed, auto and manual thresholding methods were used in this study to perform segmentation of mineral matrix pore and organic matter pore based on SEM images. By comparing results obtained from all of these methods, the conclusion drawn was that the manual thresholding method could reflect pores with diameters larger than 1 nm and identify the organic matter, pores and brittle minerals accurately by selecting a suitable segmentation thresholding value, guaranteeing the analysis to be closer to the true states. The proposed method provides a more effective method for quantitative analyses of shale pore structures.