Atmospheric intermediate volatile organic compounds （IVOCs） are complex mixtures. Due to the limited separation and identification capabilities of one-dimensional gas chromatography （¹D-GC）， a large portion of atmospheric IVOCs—which often elute as unresolved or complex peaks—are categorized as an unspeciated complex mixture （UCM）. This constrains the accurate apportionment of atmospheric IVOCs. To address this problem， an alternative analytical method has been developed utilizing thermal desorption-flow modulation comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry （TD-FM GC×GC-TOF MS） to measure atmospheric IVOCs. Analytical optimization focused on fill and flush time within a 3-second modulation period， with optimal values determined as 2 870 ms and 130 ms， respectively， to maximize separation efficiency and signal response. Compounds were separated on a ZB-5HT column （20 m×0.18 mm×0.18 μm） as the first dimension， with a BP-50 column （5 m×0.25 mm×0.20 μm） serving as the second dimension. Helium was employed as the carrier gas with column pressures maintained at 254.4 kPa （first dimension） and 202.1 kPa （second dimension）. The following temperature program was used： 50 ℃ for 10 min， then increased to 300 ℃ at 10 ℃/min， with the final temperature held for 20 min. The MS was operated in electron impact （EI， 70 eV） ionization mode. Both the ion source and transfer line temperatures were set at 300 ℃. MS signals were recorded in full scan mode with a scan range of m/z 40 to m/z 800. During thermal desorption， the desorption temperature was set at 320 ℃， and the cold trap temperature was maintained at -10 ℃ to capture desorbed targets. The secondary desorption flow rate was set at 16 mL/min. Under these optimized conditions， the method demonstrated acceptable linearity， with correlation coefficients ranging from 0.922 3 to 0.998 4， for 69 selected targets spanning 1 to 20 ng/tube， with method detection limits （spiked at 1 ng/tube） between 0.010 7 and 0.410 1 ng/m³， with recoveries ranging from 80.4% to 136.0%. Relative standard deviation values among replicate samples （n=7） spiked at 1 ng/tube， 3 ng/tube， and 10 ng/tube levels were around 4.5%-33.9%， 3.2%-19.9% and 3.5%-18.6%， respectively. Application of the method to atmospheric IVOC samples collected from an urban site of Shanghai， revealed total IVOCs mass concentrations of 8.6-61.1 μg/m³. Of these， mass concentrations of 853 individual species identified by the present method comprised 96.2% of total IVOCs. Consequently，the newly developed method improved the identification rate for UCM. Importantly， the newly speciated aromatics， chlorinated IVOCs， and oxygenated IVOCs exhibited different emission sources distinct from those routinely monitored compounds. Therefore， this study established a reliable method for determining atmospheric IVOCs， offering strong data support for precise source apportionment of complex IVOCs in the atmosphere. Additionally， this method can be used to monitor IVOCs across various environmental metrics， thereby providing essential data to support the management and control of these compounds.