<p>Shallow biogenic gas, an unconventional clean energy resource, is expected to play a pivotal role in future energy exploration and sustainable development. However, the pore characteristics and controlling factors of weakly consolidated mudstone in shallow biogenic gas systems remain unclear, hindering the prediction of gas migration pathways and storage in reservoir evaluation and development. In this study, field-emission scanning electron microscopy and gas adsorption analyses, combined with multifractal theory, were used to quantify the heterogeneity of pore structures in shallow weakly consolidated mudstone in the Hetao Basin. We further discussed the key factors controlling pore structure. The results indicated that interparticle pores dominate the pore system. Micropores show higher connectivity (<i>H</i> = 0.970−0.974, avg. 0.972), whereas meso–macropores exhibit greater heterogeneity (Δ<i>α</i> = 0.761−0.832, avg. 0.803), reflecting scale-dependent reservoir functions. Mineral composition, especially clay and quartz, primarily controls pore heterogeneity. Through comparative analysis of shales under different conditions, we identified diagenesis, mineral composition, organic matter content, and thermal maturation evolution as the key factors controlling pore heterogeneity. This study improves understanding of pore characteristics in unconsolidated mudrock reservoirs within shallow biogenic gas systems. The results can aid in predicting gas migration and storage and support exploration and development.</p>