Phthalic acid esters (PAEs) are typical organic pollutants widely distributed in various environments, including soil, water, atmosphere and sediments, etc. Meanwhile, PAEs are well known to have endocrine disruption and toxicological effects of teratogenicity, carcinogenicity and mutagenicity, causing great threats to human health and ecosystem security. In this paper, we review the distribution characteristics of PAEs pollution in the soil- plant system, summarize the multi-interfacial (soil-air, soil-water and soil-plant) migration and transformation of PAEs in the soil and its function mechanism, the in vivo metabolism, microbial degradation process and interactive mechanisms of PAEs, compared and analyzed the bioavailability of PAEs in soils, the toxicological effects at different physiological-biochemical and tissues levels, and the effects of PAEs on microbial ecological function, elaborated the pivotal techniques for preventing and control of PAEs pollution and novel strategies of agronomic regulation, and proposed the research trends on migration and transformation of PAEs in soils and associated bioavailability problems.