Since the introduction of the positive list system (PLS) for agricultural products in the Republic of Korea, the demand for a quick, easy multi-residue analysis method increased continuously. Herein, the quick, easy, cheap, effective, rugged, and safe (QuEChERS) technique combined with liquid chromatography–tandem mass spectrometry was employed to optimize a method for the multi-residue analysis of 287 pesticide residues in mandarin orange and grapefruit. Method validation was conducted in terms of selectivity, limit of quantitation (LOQ), linearity, accuracy, precision, and matrix effect. All the compounds at low spiking levels (1, 2.5, 5, or 10 mg/kg) could be quantified at LOQs lower than 0.01 mg/kg (PLS level). The linearity of the matrix-matched calibration curve for each compound is in the range 0.5–50 μg/L, and its coefficient of determination (R2) is >0.990. Satisfactory recovery values of 70–120% with a relative standard deviation of ≤20% are obtained for all compounds in the mandarin orange and grapefruit samples. A negligible matrix effect (−20–20%) is observed for more than 94.8% and 85.4% of the pesticides in mandarin orange and grapefruit, respectively. Therefore, this analytical method can contribute to pesticide residue analyses of citrus fruits for routine laboratory testing.