Due to the increasing global population and limited land resources, continuous cropping has become common. However, after a few years of continuous cropping, obstacles often arise that cause soil degeneration, decreased crop yield and quality, and increased disease incidence, resulting in significant economic losses. It is essential to understand the causes and mitigation mechanisms of continuous cropping obstacles (CCOs) and then develop appropriate methods to overcome them. This review systematically summarizes the causes and mitigation measures of soil degradation in continuous cropping through a meta-analysis. It was concluded that not all continuous cropping systems are prone to CCOs. Therefore, it is necessary to grasp the principles governing the occurrence of diseases caused by soilborne pathogens in different cropping systems, consider plant–soil-organisms interactions as a system, scientifically regulate the physical and chemical properties of soils from a systems perspective, and then regulate the structure of microbial food webs in the soil to achieve a reduction in diseases caused by soilborne pathogens and increase crop yield ultimately. This review provides reference data and guidance for addressing this fundamental problem.