In this study, small angle X-ray scattering (SAXS), scanning electron microscopy (SEM), and atomic force microscopy (AFM) were used to investigate the microstructure, spatial structure, and structural rigidity of the particles in the particulate matter (PM) produced at different exhaust gas recirculation (EGR) rates, exhaust compositions and temperatures as well as the size and number of gaps in the aggregates. The results showed that with increasing EGR rate and exhaust temperature, the aggregate size of the PM and the number of primary carbon particles increased significantly, the electronic density difference in the PM decreased gradually, the statistical mean distance between the PM decreased, the size and number of gaps in the aggregates decreased significantly, the spatial structure gradually became tighter, the Young's moduli of the powders increased gradually, the structural rigidity increased, the liquid bridge force and the van der Waals force increased gradually, the type of cohesive force changed from the liquid bridge force to a combination of the liquid bridge force and the van der Waals force, and the van der Waals force played a more prominent role. In contrast to the particles that formed due to the introduction of exhaust gas, the particles that formed due to the introduction of CO2 exhibited a chain structure, and the cohesive force decreased significantly, which resulted in loose particle packing. The particles that formed due to the introduction of only N-2 mainly exhibited a clustered structure, the cohesive force did not change significantly, and the primary carbon particles were tightly packed. The particle gap sizes ranged from 4 to 6 nm, 3 to 4 nm and 11 to 13 nm when exhaust gas, N-2 and CO2 were introduced, respectively. The N-2 in the exhaust gas was the main factor responsible for the aggregation of particles and the improvement of the structural rigidity, whereas CO2 in the exhaust gas increased the statistical mean distance between the particles and decreased the packing density of the structure and the structural rigidity.