The pore structure and its complexity play a critical role in fluid migration and recovery efficiency. Multiple pore types, broad pore size distribution (PSD), and extremely irregular pore morphology hinder the comprehensive investigation of pore systems and their complexity in low-permeability conglomerates. In this study, the multi-scale pore system and fractal characteristics of the Permian Lower Wuerhe Formation and Triassic Baikouquan Formation conglomerates from the Junggar Basin were investigated, combining physical property analysis, casting thin sections, scanning electron microscopy, and Nuclear magnetic resonance (NMR). The results show that the pore system of conglomerates consists of residual intergranular pores (RIPs), dissolution pores (DPs), clay-related pores (CRPs), and microfractures. Three types of PSD were identified according to the shape of the T2 spectrum. Based on the fractal characteristics derived from NMR data, pore systems in conglomerates were divided into macropores (mainly RIPs and DPs), mesopores (mainly CRPs), and micropores (reflect adsorption spaces). The fractal dimension of macropores (D3) increases with the increase of clay mineral content and the decrease of contents of quartz and feldspar. Moreover, the volume of macropores decreases with the increase of clay mineral content and the decrease of contents of quartz and feldspar. In addition, the fractal dimensions and volumes of mesopores and micropores have no obvious relationship with mineral composition. D3 and macropore volume control the physical properties and fluid mobility of conglomerates. T2,gm shows a strong negative correlation with D3 and macropore volume. Meanwhile, the high value of D3 would reduce the volume of macropores. These results demonstrate that D3 is a good indicator to reveal the quality of pore structure in low-permeability conglomerates.