Using mudstone and shale samples of the Qiongzhusi Formation in the Qujing area of Yunnan Province as an example, the types and characteristics of microscopic reservoir space of the shales were investigated by combined methods, including Argon ion polishing-field emission scanning electron microscopy (FESEM), high-pressure mercury injection and conventional scanning electron microscopy (SEM). Results show that the pores in shale samples of the Qiongzhusi Formation have complex formation mechanisms and different types including organic pores, clay mineral pores, grain mineral pores and microfratures, of which the organic pores dominate. The porosity is between 1.59%-11.33% with an average value of 5.0%. The reservoir space proportions of micro- and transitional pores are about 56.5%, mesopores and macropores are about 34.0%, while macropores are relatively undeveloped. TOC contents, mineral compositions and diagenesis are the main controlling factors for the development of shale pores in the Qiongzhu Formation. TOC is the main control for the development of shale pores in the Qiongzhu Formation.