There is currently a growing need to process heavier and tougher feedstocks with increased nitrogen content for fluid catalytic cracking (FCC) units. A coker gas oil with high nitrogen content was catalytically cracked in a pilot-scale riser FCC apparatus under different conditions based on different FCC processes. Then the nitrogen balance and the conversion of saturates, aromatics, resins, and asphaltenes (SARA) were calculated, and the acid amounts of coked catalysts were analyzed by the NH3-TPD method. The results show that in the synergistic process the adsorption of nitrogen-containing species on the catalyst was controlled and more acid sites were available, thus more nitrogen-free hydrocarbons, mainly the saturates, could be cracked, while the nitrogen compounds were enriched in the cracked heavy oil. Furthermore, the compositional and structural identification of nitrogen compounds in cracked heavy oils was carried out by electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Six nitrogen class species, N-1, N-2, N1O1, N1O2, N1S1, and N1O1S1, were assigned in the positive-ion spectrum, while only three class species, N-1, N-1, O-1, and N1S1, were assigned in the negative-ion spectrum. The N-1 class nitrogen compounds were the dominant species, and the N1O1S1 species were generated during the FCC process. Most of the nitrogen-containing species were 4-5 rings with short alkyl side chains. The MS data also show that the synergistic process not only inhibited the adsorption of nitrogen compounds on the catalyst but also changed their reaction pathways.