An in situ chemical reaction-based matrix solid-phase dispersion (MSPD) method was developed for the extraction of the hydrophilic and hydrophobic compounds in the plant Scutellariae radix. In this study, target analytes were hydrophilic and hydrophobic compounds in the S. radix, which included baicalein, wogonin, baicalin and wogonoside. Among these, baicalin and wogonoside were hydrophilic compounds while baicalein and wogonin were hydrophobic compounds. Several experimental conditions were discussed and optimized, including the type of the dispersant, the amount of the dispersant, the extraction time, the grinding time and the pH value. The optimized type of the dispersant was determined to be sodium bicarbonate and the amount was chose to be 20 mg. The optimized extraction time was 5 min, and the grinding time was 2.5 min at a pH of 7.5. The developed method simplified the pretreatment of extraction, reduced the use of samples and dispersants, and used pure water instead of organic solvents. In addition, the method revealed good linearity (r2 ≥ 0.9978) for the target analytes, with the limits of detection from 12.52 to 59.76 μg·kg−1, the limits of quantification from 41.72 to 199.20 μg·kg−1 and the method quantification limits from 0.124 to 0.292 μg·kg−1. Moreover, the recovery values of the tested compounds ranged from 86.0% to 104%. The MSPD method was successfully employed for the extraction of baicalein, wogonin, baicalin and wogonoside in S. radix.