Free fatty acids (FFA) are basic and indispensable components of medicinal plants. Many researches indicate that the efficacy of medicinal plant requires the presence of FFA. In the present study, ultrasonic-assisted extraction of FFA from Swertia species was optimized by response surface methodology (RSM), ensuring the highest FFA recoveries. A novel pre-column fluorescence labelling method using 2-(5-benzoacridine)ethyl-p-toluenesulfonate (BAETS) as a labelling reagent has been developed for highly sensitive and selective analysis of FFA by HPLC with fluorescent detection (FLD) and online mass spectrometry identification. RSM was also employed to optimize the fluorescence labelling of FFA. HPLC separation of 17 FFA derivatives was carried out on a reversed-phase Hypersil BDS C8 column (4.6 × 200 mm, 5 μm, Agilent Co.) with a gradient elution. The detection limits and quantifications were as low as 0.60 and 1.22 ng mL−1, respectively. FFA analysis from nine Swertia species was performed by the newly developed method, and the FFA composition of these Swertia samples was first reported.