<p>The strong heterogeneity of pores in marine–continental transitional shale reservoirs significantly restricts the efficient development of deep shale gas. Fractal dimension is a key parameter for effectively quantifying and characterizing the complexity of shale pore structure. The low-temperature CO₂/N₂ adsorption, high-pressure mercury intrusion, and nuclear magnetic resonance multi-scale characterization combined with fractal geometry theory were conducted to elucidate the mechanisms controlling fractal characteristics of macro-, meso-, micropores in this study. The multi-scale fractal dimension for each pore size range was determined using the thermodynamic model, the Menger sponge model, and the Frenkel–Halsey–Hill model, respectively. Multi-scale fractal analysis revealed micropore fractal dimension (<i>D</i>_C) was governed by TOC and clay mineral interactions. Organic matter stacking reduced surface heterogeneity, whereas clay content exceeding 50% induced hydration-driven composite pores enhancing <i>D</i>_C. Mesopore evolution (<i>D</i>_N) reflected dynamic equilibrium between organic shrinkage fractures and diagenetic processes. When TOC &lt; 10%, heterogeneity was amplified through clay–organic interactions, whereas carbonate content &gt; 10% reduced structural complexity via dissolution–cementation mechanisms. Macropore dynamics (<i>D</i>_M) exhibited phased evolution. Quartz–feldspar content exceeding 20% maintained structural integrity through rigid frameworks, while framboidal pyrite modulated complexity through dual pore-regulation mechanisms. The multi-scale fractal model overcame the limitations of traditional single-scale fractal analysis, and clarified the three-level fractal control mechanism of marine–continental transitional shale pores for the first time, providing key theoretical support for the differential development of deep shale gas, and has important guiding significance for shale gas exploration in Ordos Basin and analogous basins.</p>