This study introduces a novel method for detecting free glycidol and total free monochloropropanediol (MCPD) in fish and krill oil. Before analysis on high-performance liquid chromatography–tandem mass spectrometry (HPLC-MS), p-(dimethylamino)phenol was used for derivatization of these compounds, enabling the sensitive determination of these contaminants. The sample preparation procedure includes a simple, efficient pretreatment using NaCl aqueous solution extraction and C18 sorbent cleanup (for demulsification), distinguishing glycidol from MCPD under varied reaction conditions for derivatization (weak acidic and strong alkaline aqueous environments). This approach shows broad linearity from 1 to at least 256 ng·mL−1, improved sensitivity compared to standard GC-MS methods, with the limit of detection (LOD) and limit of quantification (LOQ) for MCPD and glycidol in both oil samples verified at 0.5 ng·mL−1 and 1 ng·mL−1, respectively. Different from previous HPLC-MS methods for direct detection of glycidol esters or MCPD esters, this is the first HPLC-MS method used for the detection of free glycidol and total free MCPD in edible oil. Furthermore, this method can be potentially developed for glycidol or monochloropropane diol esters, which is similar to the current official methods adopted for indirect detection of these contaminants in different food matrices. Application of this detection method to real dietary supplements (fish oil and krill oil) revealed MCPD residues in fish oil (maximum detected: 32.78 ng·mL−1) and both MCPD (maximum detected: 2767.3 ng·mL−1) and glycidol (maximum detected: 22.2 ng·mL−1) in krill oil, emphasizing its effectiveness and accuracy for assessing contamination in these supplements.