The work herein employed COMSOL Multiphysics simulation and experiment to study the temperature distribution of water in a specially designed cylindrical microwave (MW) reactor with two magnetrons. A numerical model was developed by combining three modules including radio frequency (RF), fluid heat transfer, and nonisothermal fluid flow. The experimental results of the temperature distribution corresponded with simulative values. Additional experiments and simulations of a single microwave port as well as two different combinations of ports were carried out to confirm the uniformity of the results. Results show that two parallel waveguides are better than both a single waveguide and two perpendicular waveguides in terms of uniformity and efficiency at the same incident power.