Value of the data •The data in this article present information on the sample pretreatment method, instrumental analysis and method validation for determination of persistent organic pollutants (POPs) in serum samples. These data provide a reference for other scientists to optimize and validate pretreatment and quantification methods in human biomonitoring studies of POPs. •The data provide information on the distributions of the total dioxin equivalents (TEQs) levels of DL-PCBs in primary ovarian insufficiency (POI) cases and controls in China, which are complementary to the article of Pan et al. These data can be used to compare TEQ levels among different populations. •The PCA data are useful for understanding the multiple effects of exposure to mixtures of POPs.