The heterogeneity of shale pores, a crucial factor in the occurrence and migration of shale gas, exerts a significant impact on the pore connectivity. Pores exhibiting a range of structural attributes to the complexity of pore connectivity. A comprehensive study into the impact of pore heterogeneity on pore connectivity in shale is lacking. This study aims to explore the impact of pore heterogeneity on pore connectivity in shale and the primary controlling factors of pore connectivity. Shale pore connectivity, pore structures, mineral composition, and geochemical parameters were assessed using various tests, including spontaneous imbibition, adsorption, mercury intrusion capillary pressure (MICP), focus ion beam-scanning electron microscopy (FIB-SEM), sulfur and carbon analysis, vitrinite reflectivity, and X-ray diffraction (XRD). Pore heterogeneity was quantitatively analyzed using the multifractal dimensions method. Results show that the increased heterogeneity of pore structure and surface roughness facilitating the potential for increased connectivity. The presence of well-developed micro-mesopores within the organic matter, alongside numerous disconnected and independent pores, contributes to an increase in pore heterogeneity. Micro-mesopore structures have a more pronounced impact on pore heterogeneity than macropores. The heterogeneity of the pores is predominantly influenced by variations in the PV and SSA of micro-mesopores. Furthermore, the heightened heterogeneity of pore structure (D1) and surface roughness (D2) leads to a more complex pore structure with increased roughness, promoting the potential for enhanced connectivity through additional throats and facilitating the formation of secondary microfractures. Shale cores characterized by high total organic carbon (TOC) content, porosity, and clay mineral content are conducive to improved pore connectivity. Conversely, the increase of thermal evolution maturity of shale in the over-mature stage is not conducive to the increase of pore connectivity. Thermal evolution maturity, TOC content, and clay mineral are key factors that control pore heterogeneity, further affecting the connectivity of shale pores. High pore connectivity is conducive to spontaneous imbibition capacity and the formation of hydraulic microfractures, promoting the migration of shale gas.