New graphene Schiff base iron nanocomplexes (S-792-Fe, S-550-Fe, and S-590-Fe) were designed and fabricated based on investigations of reactions mechanisms of AP pyrolysis, structural analysis of new materials and simulation results of quantum mechanics to deal with the long-standing contradiction between safety and performance for composite propellent combustion catalyst. By taking traditional catalyst Catocene as the benchmark, the S-550-Fe nanocomplexes exhibited competitive catalytic performances, much better anti-migration properties and significantly reduced impact and electrostatic sensitivities. After adding S-550-Fe, the burning rate of propellant enhanced from 13.87 to 19.77 mm s−1 at 15 MPa, and the impact and electrostatic sensitivities are improved to 50.2 cm and 172.12 mJ, respectively. The excellent catalytic performance of S-550-Fe is closely related to its molecular structure, which is manifested by an increase in charge density and a decrease in NH3 oxidation energy barriers. The promotion effects of S-550-Fe on desorption and oxidation of NH3 from the surface of AP is conducive to the rapid and complete pyrolysis of AP, which is reflected in the improvement of combustion rate and temperature gradient. The theory-driven design mode of this work may provide new pathways to tune combustion behaviors of composite propellants from the view of molecular-level insights.