Microscopic pore structures of shale are important to evaluating shale gas potential and exploitation value. Scanning electron microscopy (SEM), nitrogen sorption and mercury intrusion experiments were carried out to study microscopic pore structures and the controlling factors of Paleozoic shales in Upper Yangtze region, including Zunyi in Guizhou province and Tongjiang and Guanyuan in Sichuan province. The results show that the Upper Permian Dalong shale has low values of specific surface area and porosity, in which 10, of porosity is contributed by the pores below 100nm, and the framboid pyrite intercrystal pore is common in pore type. The Lower Silurian Longmaxi and Lower Cambrian Niutitang shales have higher specific surface and porosity than Dalong shale, in which 50,-80, of porosity is contributed by the pores less than 100nm, and kerogen pores and dissolution pores are dominant in pore type meanwhile a small amount of honeycomb pores, dissolution impressions and microfractures as well. It is demonstrated that microscopic pore structures are determined by type, dissolution and maturity of shale.