The development of efficient methods for evaluating pesticide residues is essential in order to ensure the safety and quality of agricultural products since the Republic of Korea implemented the Positive List System (PLS). The objective of this research was to establish a method for the simultaneous analysis of 322 pesticide residues in fruits and vegetables (such as coffee, potato, corn, and chili pepper), using the quick, easy, cheap, effective, rugged, and safe (QuEChERS) approach in combination with gas chromatography-tandem mass spectrometry (GC-MS/MS). This study introduces a robust, high-throughput GC-MS/MS method for screening the target pesticide residues in agricultural products, achieving the PLS criterion of 0.01 mg/kg LOQ. Despite some compounds not aligning with the CODEX recovery guideline, sufficient reproducibility was confirmed, attesting to the method’s applicability in qualitative analyses. A health risk assessment conducted using estimated daily intake/acceptable daily intake ratios indicated low risks associated with product consumption (<0.035391%), thereby confirming their safety. This efficient method holds significant implications for the safe distribution of agricultural products, including during import inspections.