Clay minerals and organic matter are commonly developed in shale sediments, and have an important influence on the pore structure and pore complexity of shale reservoirs. However, due to the complexity of shale pore structure and the diversity of influencing factors, the influence of organic matter, clay minerals and organo-clay composites on shale pore structure is still unclear. In this study, the effects of organic matter, clay minerals and organo-clay composites on pore structure and pore complexity of marine Longmaxi shale (LMX shale) and continental Ziliujing shale (ZLJ shale) were investigated qualitatively and quantitatively by field emission scanning electron microscopy (FE-SEM), N2 adsorption experiment with Frenkel-Halsey-Hill (FHH) model. The results comprehensively reveal the differential effect of organic matter and clay minerals, the most important pore-forming materials in shale, on the pore development of shale reservoir. Overall, the maceral type, maturity, illite, kaolinite and organo-clay composites are the main controlling factors for shale pore development and complexity. More specifically, maceral type and maturity have great influence on shale pore structure and pore complexity of all shale samples, while the effect of organic matter abundance could be ignored in continental shale. Solid bitumen is prone to develop secondary organic pores, while other macerals such as vitrinite and inertinite do not develop secondary pores with the increase of maturity. In the high-over mature marine LMX shale, a large number of secondary organic pores are generated after solid bitumen cracking and gas generation, which promotes the pore complexity. In the low-mature continental ZLJ shale, the solid bitumen has not reached the maturity of cracking gas, and the original bioclastic pores do not develop, leading to the weak development of organic pores and small contribution to pore complexity. Different clay mineral types have different effects on shale pore structure and pore complexity. The shale pore volume (PV) and specific surface area (SSA) increase with the increase of illite content, and the existence of illite enhances pore surface roughness and pore heterogeneity. However, the effect of kaolinite content on shale pore structure and pore complexity is completely opposite to that of illite. The formation of organo-clay composites protects the primary pores, and promotes the hydrocarbon generation and pore development of organic matter, which greatly increases the development of shale pores. The outcomes of this studies would provide better understanding on the pore formation mechanism of shale reservoir, which is of great significance for the accurate assessment of shale gas resources.