This paper proposes a high-efficiency single-mode traveling wave reactor based on a rectangular waveguide and its design method for continuous flow processing. The reactor has a large-capacity reaction chamber (1000 mm × 742.8 mm × 120 mm) that can provide high-energy-efficiency and approximately uniform microwave heating. The microwave heating uniformity is improved by maintaining single-mode microwave transmission and eliminating higher-order modes in such a multi-mode reaction chamber. The high energy efficiency of microwave heating is achieved by adopting impedance matching techniques. The incident microwave in the reactor can remain in a traveling wave state, and the power reflection can be minimized. Several numerical simulations based on multi-physics modeling are conducted to investigate the heating uniformity, the energy efficiency and the flexibility under different operation conditions. The results show the microwave energy efficiency can be higher than 99%, and meanwhile, the coefficient of temperature variation can be lower than 0.4. Furthermore, when the reactor is operated under different flow velocities and with different heating materials, both the energy efficiency and the heating uniformity can also meet the above requirements. The proposed reactor can be used in the applications such as oil processing, wastewater tackling, chemical synthesis, beverage sterilization and other microwave-assisted continuous flow processes that require high heating uniformity, high energy efficiency and good adaptability.