The aim of this paper is to investigate the effects of injection parameters and the exhaust gas recirculation (EGR) rate on the morphological characteristics of soot particulates and exhaust emissions in a common-rail direct-injection (DI) diesel engine with a piston displacement of 1.58 L. To investigate the influences of injection parameters and the EGR rate on the particulate morphology and exhaust emission characteristics, several different injection parameters and two EGR rates were investigated. The particulate morphology (including primary particles), the size of the soot agglomerates, the number of agglomerates, and the fractal dimension were also investigated under various injection strategies, pilot injection quantities, and percentage of EGR. The dependence of air pollution components in engine emissions, such as soot, nitrogen oxide (NOx), carbon monoxide (CO), and hydrocarbon (HC), upon pilot injection parameters and percentage of EGR at constant operating conditions was measured. A thermophoretic sampling method with a scanning electron microscope (SEM) was used to obtain the soot morphology characteristics. The soot quantity gradually increased with the increase of the pilot injection quantity at the EGR test. It is confirmed that the pilot injection quantity and rate of EGR strongly influenced soot morphological parameters. As the pilot injection quantity is increased, the size of the agglomerates and the number of agglomerates were gradually increased. The results of the PM morphological analysis indicate that the average radius of gyration and number of particles in the agglomerate increased with the increase of the EGR rate. These PM morphology parameters strongly influenced the soot mass, which also increased significantly with the increase of the EGR rate.