Taking the Longmaxi deep-marine shale gas reservoir in Zigong region as the research target, this paper aimed to characterize the nano-scale pore structure and investigate the reservoirs’ heterogeneity based on fractal theory. By conducting a series of experimental studies, mainly including TOC, XRD, gas adsorption (N2 and CH4), we were able to clarify the main controlling factors for the heterogeneity of deep shale pore structure. Our results indicated that the deep marine shale possessed a significant amount of organic matter, as the average TOC value is 3.68%. The XRD analysis results show that quartz and clay were the main mineral types, and the total content of these two minerals averaged 77.5%. Positive correlations were observed between TOC and quartz, while TOC decreases as the clay mineral increases, this discovery indicating that quartz is biogenic. Based on FHH (Frenkele-Halseye-Hill) method, by using the LTNA adsorption isotherms, we took relative pressure P/P0=0.5 as the boundary, then two separate fractal dimension were deduced, D1 and D2 represent the fractal characteristics of small and large pores, respectively. Our study revealed that both D1 and D2 demonstrated positive correlations with N2 adsorption pore volume and adsorption specific surface area, while negatively correlated with the adsorption average pore diameter. Moreover, the two fractal dimensions showed positive associations with TOC and quartz and negative associations with clay. Additionally, D1 and D2 also demonstrated a positive correlation with Langmuir volume. The presence of micropores was found to significantly influence the formation of an irregular pore structure in shale. As the pore size decreased, the adsorption specific surface area increased, resulting in a more intricate pore structure, and the fractal dimension of the pores elevated, ultimately. This intricate structure is beneficial for the accumulation of shale gas. These research findings offer valuable insights for the comprehensive assessment of deep shale gas, and enrich our knowledge of enrichment mechanisms in deep shale gas reservoirs.