In the past few years, high-resolution mass spectrometry techniques have shown great potential development in the field of pesticide residue analysis. This paper reviews the current state-of-art of two main high-resolution mass spectrometry techniques, time-of-flight mass spectrometry and FT Orbitrap-MS, applied to the analysis of pesticides in food-based matrices. This review briefly expounds the advantages of high-resolution mass spectrometry techniques and the prospective of its future application in the field of pesticide residue analysis.