In this study, a fast and sensitive method based on stir bar sorptive extraction (SBSE) and two-step thermal desorption coupled with online gas chromatography-mass spectrometry was established to simultaneously analyse six trace byproducts [phenyl salicylate (PS), xanthone (XA), methyl o-hydroxybenzoate (MS), 2-methyl diphenyl carbonate (PTC), methyl o-methoxybenzoate (MSME) and phenyl o-methoxybenzoate (PSME)] generated in the process of diphenyl carbonate (DPC) synthesis. Analytes were enriched with multiple sorptive stir bars simultaneously, followed by thermal desorption, cryo-focusing, and instantaneous injection, effectively solving such problems as long adsorption time and small sample volumes compared with conventional stir bars. The main factors influencing SBSE and thermal desorption were studied. Optimized stir bar extraction conditions are as follows: the volume fraction of methanol is 10%, the extraction time is 6 min, and the stirring rate is 1200 rpm at room temperature (25 °C). Optimized two-step thermal desorption conditions are as follows: in the first desorption step, the desorption temperature is 300 °C, the desorption time is 10 min, and the valve and transmission line temperature is 200 °C; in the second desorption step, the cold trap temperature is −10 °C, which is increased at a rate of 100 °C/s to 320 °C and held for 5 min. A splitless mode and a split mode with a split ratio of 20:1 are used in the first and the second desorption step, respectively. Under the optimal conditions, the six byproducts generated in the synthesis of DPC via transesterification were quantitatively analyzed by external standard method. The results showed that, within the range of 1.0−100 ng/L for all of the six transesterification byproducts, this method revealed good linearity with correlation coefficients (r) ≥0.997. The limits of detection (LODs) were between 0.054 ng/L and 0.253 ng/L, the relative standard deviations (RSD) were from 5.2% to 11.5%, and the recoveries were 81.6%−102.6% (n = 3). The method is simple, rapid and has a wide linear range, high accuracy, and sensitivity, as well as good stability. It is suitable for simultaneous, rapid and selective analysis of six trace byproducts in the process of DPC synthesis. It can also provide vigorous data support and industrialization guidance for the selection of transesterification conditions and research on the formation mechanisms, distribution regularity, and even control of transesterification byproducts.