Trace analysis of multi-targets in complex matrices such as cigarette smoke has always been a great challenge for analysts. In this paper, a high-throughput qualitative and quantitative method was developed and validated to determine 559 aroma compounds in mainstream smoke using gas chromatography-tandem mass spectrometry. Among four commonly used extraction solvents, dichloromethane showed obvious advantages in extracting the target aroma compounds with different polarity. An analyte protectant mixture consisting of 3-methoxy-1,2-propanediol, 1,2-octandiol, 1,2-nonanediol, and 1,2-tetradecanediol was first presented to compensate for the matrix effect, which was suitable for solvents of a wide polarity range such as hexane, dichloromethane, acetone, acetonitrile, and methanol. Moreover, the introduction of precolumn backflushing markedly improved the instrument robustness in analyzing complex cigarette smoke. The results showed that the system retained good stability after 30 days of injection. The proposed method performed well in terms of key validation parameters: accuracy (70.3–118.8% for 552 compounds), inter/intraday precision (0.1–10.7% and 0.2–18.2%), and sensitivity (limit of detection 0.12–102.54 ng/mL). Finally, this method was successfully applied to analyze 12 different commercial cigarette brands. The proposed method has good application prospects based on its robustness and may be used as a potential tool to transfer the cigarette design from an experience-dependent mode to a digital design mode. This method also shows potential in assaying aroma compounds in essentials, food or plant-based substrates.