This study aimed to develop a method, followed by gas chromatography-mass spectrometry, for detecting 37 pesticides in Chrysanthemum indicum (C. indicum) and investigating the decrease in the matrix-induced enhancement effect. The influence of QuEChERS extraction and matrix solid-phase dispersion (MSPD) on the recovery and matrix effect (ME) was compared. extraction and matrix solid-phase dispersion (MSPD) on the recovery and matrix effect (ME) was compared to decrease the ME. The cleanup sorbents, volume and type of solvent, and treatment time were optimized. The accuracy (as recovery), precision (as relative standard deviation, RSD), linearity, limit of quantitation, and limit of detection were determined. The recoveries at the three levels using mixed standard solution ranged between 76% and 120% with RSD ≤15%, and 76% and 120% with RSD ≤11% for MSPD and QuEChERS extraction, respectively. The results suggested that the ME for 21 pesticides was in the range of 80%–120% after MSPD and 15% after QuEChERS extraction. QuEChERS extraction was simpler and faster than MSPD. This methodology was applied in the analysis of 27 C. indicum samples; phorate was most frequently detected (63.0% of the sample).