An ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was developed for the determination of 12 carbohydrates in hydrolysate of Spirulina including rhamnose, xylose, arabinose, fructose, mannose, glucose, galactose, mannitol, ribose, fucose, glucuronic acid and galacturonic acid. Samples were extracted with deionized water using ultrasonic-assisted extraction (UAE) and hydrolysis by trifluoroacetic acid (TFA). The hydrolysate was separated on a Waters Acquity BEH Aminde column (100 mm×2.1 mm, 1.7 μm) using 10 mmol/L ammonium formate/water -10 mmol/L ammonium formate/acetonitrile solution as the mobile phase. The electrospray ionization tandem quadrupole mass spectrometric analysis was carried out in the negative ion mode using multiple reaction monitoring (MRM). The limits of detection were 0.005-0.15 mg/kg and the linear ranges were 0.05-5 mg/L. The average recoveries were 80.21%-121.6% at the spiked levels of the carbohydrates contents of 50%, 100% and 150% found in samples. The method was applied to analyze the samples of Spirulina. Fucose, galactose, arabinose, rhamnose, glucose, fructose, xylose, and ribose were detected in most of the samples, and their contents were in the range of 0.3-889.4 mg/g. The type and content of carbohydrates that can be detected in the sample were significantly different. Common characteristic peaks were identified as fucose, galactose, arabinose, rhamnose, glucose, fructose, xylose, ribosethe. However, mannitol and mannose were not detected in all samples. This developed method could provide technical support and basic data for the study of structure and activity of polysaccharide from Spirulina.