Fine characterization of pore systems and heterogeneity of shale reservoirs are significant contents of shale gas reservoir physical property research. The research on micro-control factors of low productivity in the Qiongzhusi Formation (Fm.) is still controversial. The lower Cambrian Qiongzhusi Fm. in the Qujing, Yunnan was taken as the object to investigate the influence of mineral compositions on the physical properties of the reservoir and the heterogeneity of shale, using the algorithm to improve the characterization ability of Atomic Force Microscopy (AFM). The results showed that: (1) The pores are mainly wedge-shaped pores and V-shaped pores. The pore diameter of the main pore segment ranges from 5 to 10 nm. Mesopores are mainly developed in the Qiongzhusi Fm. shale in Well QD1, with the average pore diameter of 6.08 nm. (2) Microscopic pore structure and shale surface properties show strong heterogeneity, which complicates the micro-migration of shale gas and increases the difficulty of identifying high-quality reservoirs. (3) The increase of clay mineral content intensifies the compaction and then destroys the pores. Conversely, brittle minerals can protect pores. The support and protection of brittle minerals to pores space depend on their content, mechanical properties and diagenesis. (4) Compression damage to pores, large microscopic roughness and surface fluctuations and strong pore structure heterogeneity are the reasons for the poor gas storage capacity of the Qiongzhusi Fm., which will lead to poor productivity in the Qiongzhusi Fm.