Abstract: The southern part of China abounds in water and heat resources. The development of multiple cropping systems in this region has long been recognized as a crucial strategy for safeguarding national food security. The expansion of these systems has driven the rapid growth of cover crops, positioning this region as a key production area for cover crops in China. Recently, many studies have demonstrated the critical role of cover crops in addressing challenges such as low resource use efficiency, high greenhouse gas emissions, and soil degradation in intensive cropping systems in southern China. However, in the southern regions of China, the adoption of cover crops within complex multiple cropping systems is hindered by disorganized planting systems, rigid variety selection, and insufficient farmer incentives. Although previous research has predominantly focused on single-factor or single-region analyses, the comprehensive effects of cover crops in the agroecological context of China’s southern multiple cropping systems, along with the underlying mechanisms driving high yield efficiency and carbon sequestration with emission mitigation, remain insufficiently elucidated. This review systematically examined the current status, challenges, and research advancements in cover crop integration within multiple cropping systems in southern China. The key mechanisms by which cover crops enhance productivity and sustainability were analyzed, including increasing exogenous organic matter input to improve soil physicochemical and biological properties, fostering synergistic interactions with primary crops under intercropping or rotation systems, and reducing agricultural inputs while optimizing resource use efficiency. Finally, considering the issues currently present in the development of cover crops, we suggest that when implementing the cultivation of cover crops in this region, measures should be taken to suit local conditions and seasonal factors. Starting from the regional characteristics and integrating the actual cropping systems with the dominant cultivated crops, appropriate cover crop varieties and planting patterns should be selected. By elucidating the synergies between yield efficiency and soil carbon sequestration, this study aimed to provide a theoretical foundation and practical insights to guide the green development and scalable adoption of cover crops in southern China’s agricultural systems.