Abstract: The influence of nitrogen-containing polycyclic aromatic hydrocarbons (NC-PAH) on the formation of carbonaceous mesophase remains enigmatic, despite extensive research on the production of carbonaceous materials from aromatic-rich oils. Molecular dynamics simulation was used to investigate the variations in pyrolysis behavior between PAH and NC-PAH based on the composition analysis. Through adjusting the content of NC-PAH, the influence of NC-PAH on the thermal stability of slurry oils (SOs) was evaluated by thermogravimetry, viscosity, coke value, and quinoline insoluble (QI). The morphology and structure of mesocarbon microbeads (MCMBs) prepared with SOs were measured by a polarized-light microscope, SEM, XRD, and Raman. Simulation results indicate that NC-PAH possesses much higher reactivity and tends to produce highly condensed solid and coke products. It corresponds to the QI and high viscosity in thermal stability experiments. Therefore, high concentrations of NC-PAH result in nonuniform morphology and disordered structures. In a system with low viscosity and few QIs, SO, which has a low nitrogen content (475 ppm), reacts gently to produce MCMBs with a uniform particle size (10–40 μm) and an excellent spherical shape. As NC-PAH content decreases, the crystalline size of graphitization elevates, as evidenced by parallel layers (10.472–11.764) and stack height (3.269–3.701 nm). The graphitization degree becomes worse and nonuniform with the increase of the content of NC-PAH, and the best is 20.58% evaluated by Raman spectra area ratio (AG/Aall). Overall, this work suggests a nitrogen content reference and a controlling technology of nitrogen for the preparation of superior MCMB.