Abstract: Planting area of the high value-added crops has been ever increasing in recent years, particularly with the agricultural intensification and scale. However, there is the large accumulation of the insect eggs and pathogenic bacteria in the soil during production, leading to the continuous cropping obstacles, as well as the soil borne pests and diseases. Alternatively, the soil disinfection is one of the most important measures to prevent and control the soil borne diseases and pests. However, the traditional chemical disinfection has often posed the ecological pollution and risks on the human and animal health. Therefore, it is an urgent need to develop the green and pollution-free physical prevention and control technologies. Among them, microwave soil disinfection can be one of the green physical application in sustainable agriculture. The microwave radiation can effectively kill the pests and pathogens in soil, while avoid the residual pollution of chemical agents. Microwave soil disinfection can be expected to fully meet the requirements of green agriculture. This study aims to systematically review the research progress of the microwave soil disinfection. Firstly, the thermal and non-thermal effects of the microwave radiation were introduced for the microwave technology. An analysis was made on its penetration in soil at the different frequency bands (915 and 2 450 MHz) and the application in various depths of soil. Among them, 915 MHz microwave was used to penetrate the soil at a deeper level, while 2 450 MHz microwave was suitable for the shallow disinfection. In addition, the mechanism of the microwave soil interaction was summarized to explore the influence of the microwave working parameters (frequency, power, and exposure time) and soil physical properties on the electromagnetic field distribution and disinfection. And there was the influence of the microwave treatment on the soil physicochemical properties and microbial communities. Furthermore, a comparison was provided on the technological differences between microwave soil disinfection equipment. And among them, the microwave disinfection equipment from developed countries was achieved in the commercial production. While the microwave disinfection equipment in China was still in the experimental prototype stage, indicating the significant gap in development level. Then, some main technological challenges were also proposed in the core components, such as the high-power microwave generators (microwave power supplies, and magnetrons) and intelligent control systems. Microwave disinfection shared some problems at present, including the uncontrolled depth of microwave disinfection, lack of uniformity, absence of core equipment components and intelligent systems, and insufficient ecological safety assessment. Future research should focus on the following directions: 1) Revealing the mechanism of the microwave soil interaction on the non-thermal effects; 2) Breakthrough the key technology of the microwave deep, uniform and efficient disinfection, in order to optimize the energy efficiency; 3) Accelerating the core components, such as the high-power microwave generators and the intelligent upgrade of equipment. This finding can provide the theoretical reference and technical route guidance to optimize microwave soil disinfection.