Quinones are highly reactive oxidants that pose risks of cytotoxicity and genotoxicity to the human body. Sensitive analysis of quinone pollutants by mass spectrometry remains challenging due to the very limited ionization efficiency of quinones and the long pretreatment time. Here, we developed a rapid and highly sensitive in-source microdroplet derivatization strategy for the determination of quinones in complex matrices. Triphenylphosphine was used as a novel "tag" to react with quinone for online derivatization of quinones via the microdroplet-driving conjugate addition reaction. The formation of phosphonium ions significantly increased the ionization efficiency of the quinones. The sensitivity was improved by 2-3 orders of magnitude as compared with other online derivatization methods. Optimization results showed that the nebulization gas pressure, capillary temperature, sample solvent concentration, and reagent concentration played important roles in the derivatization and ionization of the quinones. The developed method featured good linearity (R2 ≥ 0.996), high sensitivity (LODs at the nmol/L level), and qualified precision (RSDs ≤ 7.3%) for four typical quinones. The method was successfully applied to the determination of quinones in complex matrices including human serum and urine. Taking into consideration the fact that many derivatization procedures are completed in bulk solutions, the proposed in-source microdroplet derivatization method offers us an effective way for fast screening of derivatization reagents. The present work expands the utility of microdroplet chemistry as well as chemical derivatization in the analysis of trace compounds, which might have potential applications in the fields of environmental sciences and clinic analysis.