An ionic liquid-based microwave-assisted extraction method (ILMAE) was successfully applied for the extraction of taxifolin from Larix gmelinii. Different kinds of 1-alkyl-3-methylimidazolium ionic liquids with different kinds of cations and anions were studied and 1-butyl-3-methylimidazolium bromide was chosen as the optimal solvent for taxifolin extraction. The optimal conditions of ILMAE were determined by single factor experiments and Box-Behnken design as follows: [C4mim]Br concentration of 1.00 M, soaking time of 2 h, liquid-solid ratio of 15:1 mL/g, microwave irradiation power of 406 W, microwave irradiation time of 14 min. No degradation of taxifolin had been observed under the optimum conditions as evidenced from the stability studies performed with standard taxifolin. Compared with traditional solvent and methods, ILMAE provided higher extraction yield, lower energy and time consumption. The distribution of taxifolin in different parts of larch and the influences of age, orientation, and season on the accumulation of taxifolin were analyzed for the sufficient utilization of L. gmelinii.