Abstract: The shallow marine shale gas reservoirs in the Upper Ordovician Wufeng Formation and the Lower Silurian Longmaxi Formation of residual synclines in northern Guizhou have experienced episodic tectonic superimposed reformation. As a result, reservoir-preserving matching and reservoir formation and gas accumulation mechanisms are complex, leading to significant differences in development efficiency among different sub-layers. Therefore, it is of great significance to investigate the differential characteristics of interconnected pore-fracture systems in different shale sub-layers of various syncline units and gas-bearing intervals for better understanding the reservoir-forming mechanisms and optimizing reservoir targets. Taking the shallow marine shales from the Wufeng-Longmaxi formations in northern Guizhou as the research object, various methods were comprehensively applied including dynamic reconstruction of tectonic burial history and pressure evolution, whole rock X-ray diffgraction (XRD), field emission scanning electron microscopy (FE-SEM) imaging, image extraction using Image Pro Plus/Image J, high-pressure mercury intrusion, and directional spontaneous imbibition experiments. Besides, using key parameters such as the timing and amplitude of the last tectonic uplift and the average depressurization rate, the study validated the relatively superior tectonic preservation conditions of the gas-bearing unit in the Shixi syncline. On this basis, the preservation of organic matter pores and the genetic mechanism of interconnected pore-fracture systems in different sub-layers of the first member of the Wufeng-Longmaxi formations in the Shixi area were further elucidated. Specifically, in well SX1 of the Longmaxi Formation, organic matter pores were best developed in sub-layer ⑤, followed by sub-layers ③ and ④, and were least developed in sub-layers ①+②. Moreover, the proportion of rigid minerals-organic matter-clay composites in the microscopic field of view was relatively larger in sub-layers ⑤ and ③, followed by sub-layers ④ and ①+②. The spontaneous imbibition slopes parallel to beddings were 0.234 and 0.122 for sub-layers ⑤ and ③, respectively, higher than 0.090 and 0.053 for sub-layers ④ and ①+②. The average mercury withdrawal efficiency values of high-pressure mercury intrusion were 37.047% and 31.912% for sub-layers ⑤ and ③, respectively, higher than 29.48% and 27.55% for sub-layers ④ and ①+②. The findings implied that the composites contributed significantly to organic matter pore preservation and pore-fracture system connectivity. Based on these findings, the study establishes a classification scheme for the genesis of microscopic pore-fracture systems in the shallow marine shale reservoirs from the Wufeng-Longmaxi formations in northern Guizhou and clarifies their reservoir-controlling mechanisms under the coupling constraints of dynamic and static gas accumulation elements. Three genetic models of pore-fracture systems were proposed, including pore preservation and fracture development with rigid minerals-organic matter-clay composites, relative pore preservation and fracture development with rigid minerals-organic matter-clay composites, and pore collapse type with the enrichment of rigid minerals parallel to shale beddings.