Microplastics have emerged as a widespread pollutant in agricultural soils, entering primarily through plastic film mulching, sewage irrigation, and the application of organic fertilizers. Their continuous accumulation poses a growing threat to soil ecosystem health and functionality. Therefore, a deep understanding of the impact process and mechanism of microplastics on the functioning of agricultural soil ecosystems is of great scientific significance and practical value for scientifically assessing their ecological and environmental risks, developing pollution control and remediation strategies. This review systematically examines the migration and transformation behavior of microplastics in agricultural soil and analyzes their diverse ecological effects, including alterations to soil physicochemical properties, shifts in microbial communities, impacts on soil fauna, and influence on crop growth. It also synthesizes current knowledge regarding the broader implications of microplastics on soil nutrient cycling, greenhouse gas emissions, crop productivity, and overall soil health. On this basis, key scientific questions are identified in areas such as the complex environmental behavior mechanisms of microplastics in real environments, inter-trophic interactive effects, and the systematic assessment of ecological risks and soil health. Finally, future research priorities and directions are proposed to provide a theoretical foundation for risk prevention and green remediation of microplastic pollution in agricultural soils.