This paper is one of the few studies that examine the use of water-amine nanofluid along with iron oxide nanoparticles with volume fraction ϕ = 0 to 0.05 to remove acid gases (\({\text{H}}_{2}\text{S}\) and CO2) from natural gas. In this research, real-size refinery equipment was simulated using Fluent software, and the effects of nanoparticles and a constant magnetic field on increasing the heat transfer rate and the removal rate of acid gases from natural gas were investigated. The results show that in the absorption tower, with the increase of the Reynolds number from Re = 8000 to 24,000, the Nusselt number also increases, and with the rise of the \(\phi\) to 0.05, the mole fraction of \({H}_{2}S\) in the nanofluid increases to 34%, and the mole fraction of CO2 increases to 23%. Additionally, as the temperature increases, the dynamic viscosity of the nanofluid decreases. However, when the volume fraction (ϕ) increases to 0.05, the dynamic viscosity of the nanofluid approximately increases by 10% in the temperature range of 45 to 56 \({^\circ{\rm C} }\). In this research, magnetic field intensities ranging from 0 to 20,000 Gauss were used. With \(\phi\)=0.01, the mentioned magnetic fields increase the mass transfer coefficient to 13.26%. With \(\phi\) = 0.05, the mass transfer coefficient decreases to 4.44% due to the increased probability of nanoparticles settling. The maximum mass transfer coefficient is up to 67.4%, which is observed in \(\phi\) = 0.03, with the magnetic field intensity of 20,000 gauss. A limitation of this research was the failure to evaluate the effect of changing the fluid flow regime on other refinery equipment.