Fructooligosaccharides (FOS), which are regarded as functional ingredients, are commonly classified as dietary fibers in many countries. However, few analytical methods for separation and analysis of individual FOS in plants, crops, and food products have been developed. In this study, a simple, rapid, and sensitive high performance liquid chromatography with charged aerosol detector (HPLC-CAD) method was developed for simultaneous determination of 11 inulin-type FOS with degree of polymerization (DP) 3-13 in different samples. The separation was performed on a Waters XBridge Amide column (4.6 × 250 mm i.d., 3.5 μm) with gradient elution. All calibration curves for investigated analytes showed good linear regression (R > 0.9962). Their limits of detection (LOD) and quantification (LOQ) were in the ranges 0.4-0.6 μg/mL and 1.4-2.3 μg/mL, respectively. The recoveries ranged from 94.0% to 114.4%. A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was applied to qualitative analysis of FOS in different samples. The developed method was successfully applied to analysis of 11 FOS in different samples of plants from Compositae, Campanulaceae, and Rubiaceae families. The developed HPLC-CAD nethod with microwave-assisted extraction can be used for quantitative analysis of FOS and is helpful for quality control of plants containing FOS.