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In recent years, the shale gas in the southern Sichuan Basin has achieved great commercial development, and the Silurian Longmaxi Formation is the main development stratum. In order to solve the problems of great difference production and inaccurate gas content of the Longmaxi Formation shale gas field in the southern Sichuan Basin, based on thin section identification, argon ion polishing-field emission scanning electron microscopy, high pressure mercury injection, low temperature nitrogen adsorption and the fractal method, the micropore structural heterogeneity of the siliceous shale reservoir of the Longmaxi Formation has been studied. The results show the following: The pores of siliceous shale are mainly intergranular pores and organic pores. Image analysis shows that there are obvious differences in size and distribution of shale pores among different types. The micropore structural heterogeneity is as follows: intragranular pore > intergranular pore > organic pore. In the paper, the combination of low temperature nitrogen adsorption method and high-pressure mercury injection method is proposed to characterize the micropore size distribution and fractal dimension, which ensures the credibility of pore heterogeneity. The shale pores are mainly composed of mesopores (2–20 nm), followed by macropores (100–300 nm). For different pore sizes, the fractal dimension from large to small is mesopore, micropore and macropore. Shale pore structure and fractal dimension are correlated with mineral composition and total organic carbon (TOC) content, but the correlation is significantly different in different areas, being mainly controlled by the sedimentary environment and diagenesis. [ABSTRACT FROM AUTHOR]