The multifractal structure of shale pores significantly affects the occurrence of fluids and the permeability of shale reservoirs. However, there are few studies on the multifractal characteristics of shale pores that distinguish between organic and inorganic pores. In this study, we obtained the pore size distribution (PSD) of organic and inorganic shale pores separately by using a new NMR-based method and conducted a multifractal analysis of the structure of organic and inorganic shale pores based on PSD. We then investigated the geological significance of the multifractal characteristics of organic and inorganic shale pores using two multifractal characteristic parameters. The results showed that the structures of both organic and inorganic pores have multifractal characteristics. Inorganic pores have stronger heterogeneity and poorer connectivity compared to organic pores. The multifractal characteristics of inorganic pores significantly affect shale permeability and irreducible water saturation. Greater heterogeneity in the inorganic pore structure results in lower shale permeability and higher irreducible water saturation. Meanwhile, better connectivity leads to higher shale permeability and lower irreducible water saturation. The multifractal characteristics of organic pores significantly affect the shale adsorption capacity and have a weak impact on irreducible water saturation. Greater heterogeneity in the organic pore structure results in the shale having stronger adsorption capacity and higher irreducible water saturation The results also indicate that the multifractal characteristic parameters of inorganic pores can be regarded as an index for estimating the irreducible water saturation and flowback rate of fracturing fluid, and the multifractal characteristic parameters of organic pores can be regarded as an index for evaluating the quality of shale reservoirs.