Investigation of the combustion process in nanofluids consisting of oxygen molecules and aluminum nanoparticles indicates the factors affecting this process and, as a result, creates a phase change in the simulated atomic structure. In this study, using molecular dynamics simulations, the combustion process in nanofluids, including oxygen molecules and aluminum nanoparticles, was studied from an atomic point of view. The physical equilibrium in atomic samples was initially investigated by examining atomic structures’ kinetic energy and potential energy. Kinetic energy and potential energy were balanced at 77.02 eV and −6769.58 eV, respectively. This convergence in the expressed physical quantities indicated that the atomic structure of the prototype and the interaction between the atomic structures were well selected. Also, some factors such as changes in initial temperature and pressure and the change in applied external heat flux to the nanofluid led to the optimal conditions for combustion in the atomic structure and processes such as heat transfer. As the initial temperature rises to 400 K, the flux in the atomic sample and the combustion time converged to 1289 Wm-2 and 6.29 ns, respectively. And with increasing pressure in atomic samples to 6 bar, atomic oscillations decrease. Also, the flowing flux in the atomic sample and the combustion time converged to 1383 Wm-2 and 5.5.31 ns with increasing external heat flux.