The new version of the industrial ammonia synthesis reactor has three catalyst beds with two dimensional flows and there is a cooler after adiabatic beds. The feed gas is preheated in two middle heat exchangers with high temperature gas product. The gas flows along the length and radius of the bed by embedding a gas channel around the bed, which has no holes at the beginning, and gas does not flow radially in this part. After, gas goes radially to the bed and leaves from the perforated middle tube. In this study, a three-bed ammonia reactor with radial axial flow with two heat exchangers in the middle has been studied. This reactor is different from the previous generation in terms of its fluid regime having two-dimensional axial radial flow and an intercooler. Two-dimensional mathematical modeling is applied for the prediction of fluid flow, concentration, and temperature profiles along the reactor. The Navier-Stokes, mass, and heat partial differential equations are solved simultaneously via orthogonal collocation on the finite element method. The results have been compared with industrial data and good agreement has been observed.