Micropores of shale are significant to the gas content and production potential of shale, which has been verified in the research of marine shale gas; while, few studies have been conducted on lacustrine shales. This study collected 42 samples from three wells in the Late Cretaceous Qingshankou Formation of the southern Songliao Basin, NE China, and investigated these samples by the focused ion beam-scanning electron microscope (FIB–SEM) and nitrogen adsorption analysis techniques. Four types of micropores were identified in the samples, i.e., intergranular pore, intracellular pore, organic matter pore and microfracture. The pore structure type is characterized by open slit pores and “ink type” pores which are mainly 1.5–5 nm in diameter with mesopores as the main pores. The mesopores account for 74.01% of the pore volume and 54.68% of the pore surface area. Compared with the lacustrine shales from the Triassic Yanchang Formation in the Ordos Basin and Xujiahe Formation in the Sichuan Basin, the intergranular clay mineral interlayer pores are considered to be the main reservoir space for shale gas storage in the study area, followed by intraparticle pores, organic matter pores and microfractures. Maturity and micropore are the key controlling factors which affect the shale gas content of the Qingshankou Formation in southern Songliao Basin.