Atmospheric oxidation products of volatile organic compounds consist of thousands of unique chemicals that have distinctly different physical and chemical properties depending on their detailed structures and functional groups. Measurement techniques that can achieve molecular characterizations with details down to functional groups (i.e., isomer-resolved resolution) are consequently necessary to provide understandings of differences of fate and transport within isomers produced in the oxidation process. We demonstrate a new instrument coupling the thermal desorption aerosol gas chromatograph (TAG), which enables the separation of isomers, with the high-resolution time-of-flight chemical ionization mass spectrometer (HR-ToF-CIMS), which has the capability of classifying unknown compounds by their molecular formulas, and the flame ionization detector (FID), which provides a near-universal response to organic compounds. The TAG-CIMS/FID is used to provide isomer-resolved measurements of samples from liquid standard injections and particle-phase organics generated in oxidation flow reactors. By coupling a TAG to a CIMS, the CIMS is enhanced with an additional dimension of information (resolution of individual molecules) at the cost of time resolution (i.e., one sample per hour instead of per minute). We found that isomers are prevalent in sample matrix with an average number of three to five isomers per formula depending on the precursors in the oxidation experiments. Additionally, a multi-reagent ionization mode is investigated in which both zero air and iodide are introduced as reagent ions, to examine the feasibility of extending the use of an individual CIMS to a broader range of analytes with still selective reagent ions. While this approach reduces iodide-adduct ions by a factor of 2, [M − H]− and [M + O2]− ions produced from lower-polarity compounds increase by a factor of 5 to 10, improving their detection by CIMS. The method expands the range of detected chemical species by using two chemical ionization reagents simultaneously, which is enabled by the pre-separation of analyte molecules before ionization.