Herein, a method of ultrasound treatment combined with surfactant aqueous phase dispersion was proposed for the extraction of high-purity gutta-percha in its native state from enzymatic hydrolyzed Eucommia ulmoides pericarps. Firstly, the plant tissues wrapped around gutta-percha were destructed through enzymatic hydrolysis, then the plant tissues debris still attached to gutta-percha were further stripped off by ultrasound. Finally, under the “amphiphilic” action of sodium dodecyl sulfate (SDS), the entangled gutta-percha was untwined, allowing the residual plant tissue debris to be released and precipitated, thus high purity gutta-percha was obtained. The process parameters were optimized through single factor and response surface experiments. The optimal parameters for ultrasonic treatment were displayed as follows: frequency of 40 kHz, power of 320 W, time of 7.3 h, temperature of 50 °C, and material-to-liquid ratio of 1:70 g/mL, and for the aqueous phase dispersion of surfactant were SDS concentration 1.7%, temperature 80 °C, stirring speed 1200 rpm, solid-to-liquid ratio 1:60 g/mL, and time 60 h. Under optimal conditions, the purity of gutta-percha reached 95.4 ± 0.31% and its weight average molecular weight (Mw) was 20.85 × 104. Moreover, the obtained gutta-percha maintained its native filamentous form. The obtained products were characterized by IR, NMR, XRD, TGA, DSC, and tensile experiments, which showed that the obtained product was gutta-percha and maintained the natural α- and β- crystal structure. The proposed method overcomes the disadvantages of the traditional organic solvent method, which has great environmental pollution and destroys the gutta-percha structure. This is also the first reported method to obtain high purity gutta-percha while maintaining its native state.