Highly polar pesticides (HPP) are a group of pesticides that are characterize as low Log Kow. Many high-throughput multi-residue analysis methods based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) for the simultaneous determination of such polar pesticides have been proposed. In this article, we summarize the various sample preparation methods including quick polar pesticides (QuPPe), dispersive solid phase extraction (dSPE), solid phase extraction (SPE) and QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe), especially for QuPPe, which are mainly used for the determination of HPP in foods. In addition, we summarize LC-based separation methodologies that are currently used for the analysis of HPP in foods, including reversed-phase chromatography (RPC), hydrophilic interaction liquid chromatography (HILIC), ion chromatography (IC) and mixed-mode chromatography (MMC). Finally, the current mass spectrometry-based methodologies for the analysis of HPP are summarized with a specific focus on MS configurations and acquisition modes.