The detection of trace aroma compounds in samples with complex matrices such as Chinese liquor (Baijiu) requires a combination of several methods, which makes the analysis process very complicated. Therefore, a headspace solid-phase microextraction (HS-SPME) method coupled with two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOFMS) was developed for the quantitation of a large number of trace compounds in Baijiu. Optimization of extraction conditions via a series of experiments revealed that dilution of the alcohol content of 8 mL of Baijiu to 5%, followed by the addition of 3.0 g of NaCl and subsequent SPME extraction with DVB/CAR/PDMS fiber coating over 45 min at 45 °C was the most suitable. To check the matrix effects, various model Baijiu matrices were investigated in detail. The quantitative method was established through an optimized model synthetic solution, which can identify 119 aroma compounds (esters, alcohols, fatty acids, aldehydes and ketones, furans, pyrazines, sulfur compounds, phenols, terpenes, and lactones) in the Baijiu sample. The developed procedure provided high recovery (86.79–117.94%), good repeatability (relative standard deviation < 9.93%), high linearity (R2 > 0.99), and lower detection limits than reported methods. The method was successfully applied to study the composition of volatile compounds in different types of Baijiu. This research indicated that the optimized HS-SPME–GC×GC-TOFMS method was a valid and accurate procedure for the simultaneous determination of different types of trace compounds in Baijiu. This developed method will allow an improved analysis of other samples with complex matrices.