In recent years, food safety issue has become one of the focuses of global concerns. Chromatography as the most common method has been applied to detecting harmful substances in food widely. However, chromatographic methods used in the detection of analytes with the characteristic of low molecular weight, high polarity, low volatility, thermal instability, less chromophore will encounter some problems such as low detection response and low retention time. While, derivatization is a common means to solve these problems. In this paper, we mainly introduced derivative reagents and derivatization methods in sample preparation. The applications of derivatization techniques in chromatographic analysis of mycotoxins, illegal additives, pesticide and veterinary drug residues, and so on in food samples were reviewed.