Abstract: With the increasing development of isotope analysis technology, compound-specific isotope analysis (CSIA) has become an advantaged analysis technology with high-resolution and high-sensitivity, and has gradually attracted great attention. At present, the application of CSIA in the origin traceability of organic pollutants mainly focus on in halohydrocarbons, PAHs and MTBE, and its application in the field of pesticide residue traceability remains to be researched. The application of CSIA in the traceability of organic pollutants (e.g. halohydrocarbons, PAHs and MTBE) is summarized in this review, which includes discussion about the problems existing in the traceability of organic pollutants, and application prospect in the field of pesticide residue traceability, which provides a reference for the development and application of CSIA in the traceability of food (especially agricultural products, etc.) pollutants.