Objective To explore the seed protein extraction method for Amomum villosum Lour., so as to lay the foundation for the study of differential proteomics of Amomum villosum Lour. during seed dormancy and germination. Methods We used the four kinds of commonly-used protein extraction methods for the experiment, including Tris-HCl extraction method, trichloroacetic acid (TCA) /acetone precipitation method, direct lysis buffer method and improved Tris-saturated phenol method. The obtained proteins were quantified, and then were analyzed by sodium dodecyl sulphate- polyacrylamide gel electrophoresis (SDS-PAGE) . Results The protein yield was the highest when using direct lysis buffer method, which was mainly composed of small molecule protein. The protein yield was the lowest using Tris/HCl method, characterized by the diffused stripes in SDS-PAGE spectra. The protein yield was moderate using TCA/acetone method and improved Tris-saturated phenol method, and the obtained protein by the TCA/acetone method had less stripes in SDS-PAGE spectra than that by Tris-saturated phenol method, and was characterized by macromolecular protein. Conclusion The combination of direct lysis buffer extraction method and improved Tris-saturated phenol method may provide reference for seed protein extraction method of two-dimensional electrophoresis for Amomum villosum Lour..