In this work, we reported a stable isotope labelling-flow injection analysis-mass spectrometry (SIL-FIA-MS) method for high throughput analysis of 5-hydroxymethylfurfural (HMF) content in drinks. 3-Nitrophenylhydrazine (3-NPH) and 13 C 6 -3-Nitrophenylhydrazine hydrochloride ( 13 C 6 -3-NPH) were used as pared labelling reagents to selectively label HMF. With a simple centrifugal operation, a certain volume of sample was directly mixed with 3-NPH solution. After adding a small amount of 13 C 6 -3-NPH labelled HMF as internal standard, the sample can be directly transferred for the subsequent MS analysis owing to the contamination-free feature of excess 3-NPH. By using a multi-well thermostatic oscillator to carry out bath derivatization, the average time cost for each sample pretreatment was less than 1 min. Coupled with a triple-quadrupole mass spectrometer, FIA-MS with multiple reaction monitoring (MRM) was used for the rapid and high throughput detection of the labelled HMF in negative ion mode. The time cost for MS detection including injection process for each sample was about 1.5 min. Namely, the whole procedure including sample pretreatment and MS detection can be completed within 3 min per sample, which was very suitable for routine analysis for its high throughput and simplification. By labelling HMF with 3-NPH, the characteristic fragment ion after labelling and detection in interference-lesser negative ion mode enabled high detection specificity even without chromatographic separation. By using 13 C 6 -3-NPH labelled HMF as internal standard to counteract the matrix effect during MS analysis, the detection accuracy and precision were guaranteed. In order to achieve the best conditions for the derivatization of HMF, several derivatization conditions including the acid concentration, the proportion of acetonitrile (ACN), the derivatization reagent concentration, reaction temperature and reaction time were investigated in detail. Under the optimized derivatization, quantitative analysis method was validated in ranges of 0.050–5.0 μg/mL. The relative standard deviations (RSDs) of inter-day and intra-day precision were less than 5.42% and 4.89%, respectively, showing satisfied reproducibility. The proposed method has been successfully applied to the analysis of HMF in sugar-sweetened drinks for feasibility verification in real samples. • SIL-FIA-MS was realized by using MS response-free and contamination-free 3-NPH and 13 C 6 -3-NPH for labelling. • Rapid and high throughput MS analysis for HMF was realized. • The method also offers competitive advantages in accuracy, specificity, simplification, automatability and LODs. • The method is promising to determine other aldehydes in foods with proper modifications.