Purpose The widespread usage of magnetic nanoparticles (MNPs) requires their efficient synthesis during combustion process. This study aims to present a mathematical model for the oxidation of MNPs in a counter-flow non-premixed combustion system to produce MNPs, where the key sub-processes during the oxidation reaction are involved. Design/methodology/approach To accurately describe structure of flame and determine distributions of temperature and mass fractions of both reactants and products, equations of energy and mass conservations were solved based on the prevailing assumptions that three regions, i.e. preheating, reaction and oxidizer zones exist. Findings The numerical simulation was first validated against experimental data and characteristics of the combustion process are discussed. Eventually, the influences of crucial parameters such as reactant Lewis numbers, strain rate ratio, particle size, inert gas and thermophoretic force on structure of flame and combustion behavior were examined. The results show that maximum flame temperature can achieve 2,205 K. Replacing nitrogen with argon and helium as carrier gases can increase flame temperature by about 27% and 34%, respectively. Additionally, maximum absolute thermophoretic force was found at approximately 9.6 × 10–8 N. Originality/value To the best of authors’ knowledge, this is the first time to numerically model the preparation of MNPs in a counter-flow non-premixed combustion configuration, which can guide large-scale experimental work in a more effective way.