Radix Isatidis has widely useful activities including anti-virus, anti-bacterial. Tryptanthrin, indigo, and indirubin are active ingredients in R. Isatidis. Response surface methodology (RSM)-optimized infrared-assisted extraction (IRAE) was developed and combined with HPLC for simultaneous determination of tryptanthrin, indigo, and indirubin from R. Isatidis. IRAE were investigated through extraction yields of the three components and optimized by RSM. The optimum conditions were as follows: infrared power of 129 W, solid/liquid ratio of 1:40 g/mL, and irradiation time of 22.5 min. IRAE conditions obtained by RSM were not only accurate, but also had practical value reflecting the expected optimization. Subsequently, this novel IRAE method was evaluated by extraction yield of the components of R. Isatidis samples from different regions. Compared with common extraction methods including maceration extraction (ME), reflux extraction (RE), ultrasound-assisted extraction (UAE), and microwave-assisted extraction (MAE), IRAE showed higher yield with advantages of no limitation of solvent selection, low cost, convenience under optimum extraction conditions. These results suggested the potential of RSM-optimized IRAE for extraction and analysis of the water-/fat-soluble compositions of Chinese herbal medicine. A simple chromatographic separation for simultaneous determination of tryptanthrin, indigo, and indirubin from Chinese herbal medicine R. Isatidis was performed on a C18 column (Diamonsil 150 mm × 4.6 mm i.d., 5 μm) with a mobile phase isocratic consisting of methanol and water at a flow-rate of 0.8 mL min−1. The retention times of tryptanthrin, indigo, and indirubin were 15.4, 31.9, and 58.6 min, respectively. The linear equations were obtained as follows: y = −3094.5744 + 21208.792x for tryptanthrin (R = 0.9998, 0.9–18.0 μg mL−1), y = 4730.0448 + 30180.567x for indigo (R = 0.9997, 0.5–10.0 μg mL−1) and y = −6582.9045 + 67069.312x for indirubin (R = 0.9997, 0.4–8.0 μg mL−1). The result showed that RSM-optimized IRAE was a simple, efficient pretreatment method for the analysis of complex matrix.