The compressibility of shale matrix reflects the effects of reservoir lithology, material composition, pore structure and tectonic deformation. It is important to understand the factors that influence shale matrix compressibility (SMC) and their effects on pore size distribution (PSD) heterogeneity in order to evaluate the properties of unconventional reservoirs. In this study, the volumes of pores whose diameters were in the range 6–100 nm were corrected for SMC for 17 shale samples from basins in China using high-pressure mercury intrusion and low-temperature nitrogen gas adsorption analyses, in order to investigate the factors influencing the SMC values. In addition, the variations in fractal dimensions before and after pore volume correction were determined, using single and multifractal models to explain the effects of SMC on PSD heterogeneity. In this process, the applicability of each fractal model for characterizing PSD heterogeneity was determined using statistical analyses. The Menger and Sierpinski single fractal models, the thermodynamic fractal model and a multi-fractal model were all used in this study. The results showed the following. The matrix compression restricts the segmentation of the fractal dimension curves for the single fractal Menger and Sierpinski models, which leads to a uniformity of PSD heterogeneity for different pore diameters. However, matrix compression has only a weak influence on the results calculated using a thermodynamic model. The SMC clearly affects the multifractal value variations, showing that the fractal dimension values of shale samples under matrix compression are small. Overall PSD heterogeneity becomes small for pores with diameters below 100 nm and the SMC primarily affects the PSD heterogeneity of higher pore volume areas. The comparison of fractal curves before and after correction and the variance analysis indicate that the thermodynamic model is applicable to quantitatively characterize PSD heterogeneity of shale collected from this sampling area. The results show that PSD heterogeneity increases gradually as micro-pore volumes increase.