In recent years, the removal of organic pollutants from water and wastewater has attracted more attention to different advanced oxidation processes (AOPs). There has been increasing interest in using peroxyacetic acid (PAA), an emerging oxidant with low or no toxic by-products, yet the promotion and application are limited by unclear activation mechanisms and complex preparation processes. This paper synthesized the related research results reported on the removal of organic pollutants by PAA-based AOPs. Based on the research of others, this paper not only introduced the preparation method and characteristics of PAA but also summarized the mechanism and reactivity of PAA activated by the free radical pathway and discussed the main influencing factors. Furthermore, the principle and application of the newly discovered methods of non-radical activation of PAA in recent years were also reviewed for the first time. Finally, the shortcomings and development of PAA-based AOPs were discussed and prospected. This review provides a reference for the development of activated PAA technology that can be practically applied to the treatment of organic pollutants in water.