A two‐step simulation approach combining large eddy simulation (LES) for turbulent flame and multidimensional/multivariate population balance Monte Carlo (PBMC) for nanoparticle dynamics is proposed to explore the detailed flame fields and particle dynamics of zirconia nanoparticles in a flame spray pyrolysis (FSP) reactor. The turbulent combustion of gas and spray are simulated by the nonlinear LES‐partially stirred reactor model. Thereafter, the differentially weighted PBMC is applied for the first time to describe the spatially resolved formation and growth of nanoparticles using the flame fields derived from LES as an input. An efficient submodel for particle spatial transport in multidimensional grids is adopted and tested to account for the effect of thermophoresis, convective and diffusion of the nanoparticles. This methodology is successfully applied to an FSP case, demonstrating a reliable level of fidelity when compared to experiments and other model. Simulation results are discussed, in particular the flame fields and the size, morphology, as well as polydisperse primary particle and aggregates size distribution.