Microwave heating has excellent potential for applications in wastewater treatment. This study proposes a highly efficient continuous liquid-phase microwave heating system to overcome the problems of low treatment capacity, low dynamic range of loads, and insufficient heating uniformity of the existing equipment. First, a quarter-wavelength impedance-matching layer improves heating efficiency, and the heating uniformity has been enhanced by horn antennas. Second, an experimental system is developed. The simulation and experimental results are consistent, with the microwave system achieving over 90% energy utilization for different thicknesses and concentrations of salt water. Finally, simulations are performed to analyze microwave efficiency and heating uniformity at different flow rates, salinities, dielectric properties, and sawtooth structures. The system can efficiently heat loads with a wide range of dielectric properties, including saline water. Generally, when the permittivity varies from 10 to 80, and the loss tangent varies dynamically from 0.15 to 0.6, more than 90% of microwave efficiency and excellent temperature distribution (The coefficient of temperature variation COV < 0.5) can be achieved. The system’s modular design enables scaling up to further boost processing capacity. Overall, the system provides high-throughput, high-efficiency, high-uniformity, and large-dynamic-range microwave water treatment, which has promising applications in industrial water treatment.