In high-power microwave applications, the reflection of energy can be effectively reduced by adjusting the three-stub waveguide. However, most of the existing tuning algorithms do not make an arrangement for the adjustment sequence of stubs, and accurately calculating the depth of the stubs requires a great deal of time via electromagnetic (EM) simulations, which may cause large reflection in the matching process. To solve these problems, we first propose an improved calculation method that can accurately calculate the input impedance of a three-stub waveguide. Then, an impedance matching algorithm is designed based on the equivalent circuit model that can quickly and accurately calculate the optimal depth of the stubs. Finally, we present a low-reflection tuning strategy to suppress the large reflection during the adjustment of the stub process. An experimental system is built to verify the calculation method and the tuning strategy. The results show that the strategy can avoid large reflection in the case of load mutation and can maintain low reflection when the load changes continuously. The algorithm meets the needs of the industry and can be used for automatic and real-time adjustment of three-stub waveguides of different specifications.