As the two important components of shale, organic matter (OM) and clay minerals are usually thought to strongly influence the hydrocarbon generation, enrichment and exploitation. The evolution process of OM and clay minerals as well as their interrelationship over a wide range of thermal maturities are not completely clear. Taking Yanchang (T3y), Longmaxi (S1l) and Niutitang (?1n) shales as examples, we have studied the microstructure characteristics of OM and clay minerals in shales with different thermal maturities. The effects of clay minerals and OM on pores were reinforced through sedimentation experiments. Using a combination of field emission scanning electron microscopy (FE-SEM) and low-pressure N2 adsorption, we investigated the microstructure differences among the three shales. The results showed that both OM and clay minerals have strong effects on pores, and small mesopore (2–20 nm) is the dominant pore component for all three samples. However, the differences between the three samples are embodied in the distribution of pore size and the location. For the T3y shale, clay minerals are loosely arranged and develop large amounts of pores, and fine OM grains often fill in intergranular minerals or fractures. Widespread OM pores distribute irregularly in S1l shale, and most of the pores are elliptical and nondirectional. The ?1n shale is characterized by the preferred orientational OM-clay aggregates, and lots of pores in the composites are in the mesopore range, suggesting that over maturity lead to the collapse and compaction of pores under huge pressure of strata. The results of the current research imply that with increasing thermal maturity, OM pores are absent at low maturity (T3y), are maximized at high maturity (S1l) and are destroyed or compacted at over-mature stage (?1n). Meanwhile, clay minerals have gone through mineral transformation and orientational evolution. The interaction of the two processes makes a significant difference to the microstructure evolution of OM and clay minerals in shale, and the findings provide scientific foundation in better understanding diagenetic evolution and hydrocarbon generation of shale.