Insecticides, fungicides and other chemical pesticides are commonly used by grape growers to prevent and control pests and diseases, which inevitably leads to residues of harmful substances in wine, jeopardizing the quality and safety of wine. This article reviews the behavior of pesticide residues in winemaking and the influence of pesticide residues on wine flavor, with a focus on the effects of destemming and crushing, dipping, fermentation, clarification and filtration on the migration, degradation and metabolism of common pesticide residues. Meanwhile, this article also analyzes the interference of pesticide residues with the major flavor substances (alcohols, esters and volatile sulfur compounds) in wine. We expect that this review will provide reference for future studies on pesticide residues in wine for the production of safe and high-quality wine.