This study aims to develop a fast and eco-friendly liquid chromatography–mass spectrometry (LC-MS) method for the determination of aesculin and aesculetin in Cortex Fraxini. Ultrapure water was used as the solvent during the microwave-assisted extraction process to prepare the Cortex Fraxini sample. This extraction method reduces the cost of the harmful solvent (only ultrapure water was used) and microwave extraction time (1 min). The LC separation was conducted using an Agilent InfinityLab Poroshell 120 EC-C18 column (2.1 mm × 30 mm, 2.7 µm) with a mobile phase consisting of 0.1% formic acid and acetonitrile (90:10, v/v) at a flow rate of 0.6 mL/min. Isocratic elution was employed, and the analytes were detected by MS. Through careful optimization and selection of LC-MS conditions, the analysis time was reduced to 1 min, demonstrating the method’s efficiency. The developed method was validated and exhibited excellent specificity, linearity, limit, precision, accuracy, and stability in quantifying aesculin and aesculetin in the Cortex Fraxini samples. The analysis result revealed the presence of aesculin (ranging from 3.55 to 18.8 mg/g) and aesculetin (ranging from 1.01 to 16.2 mg/g) in all ten batches of Cortex Fraxini samples. Compared to the reported LC methods, this approach substantially reduces the total analysis time and requires a minuscule volume of organic solvents. An “Analytical Eco-Scale” assessment was used to evaluate the different assay methods of Cortex Fraxini. The current LC-MS method scored an impressive 90; it was better than the other four reports’ LC methods. Thus, the developed LC-MS method is rapid and green, which is helpful for the quality evaluation of Cortex Fraxini.