High-intensity pulsed electric field (PEF) was used to extract protein from mussel. Results show that PEF extraction speed is much faster, and the extraction yield of protein is higher compared with traditional methods. Variation of PEF parameters and the extraction yield of protein were determined by single-factor experiments. The processing conditions were optimized by response surface methodology. The maximum extraction yield of protein of 77.08% was achieved under the following conditions: electric field intensity of 20 kV/cm, pulse number of 8 and enzymolysis time of 2 h. PEF can be widely used to extract protein with high speed and low pollution. Practical Applications Freshwater mussel is widely cultured in China and plays a very important role in aquaculture business. Recently, thanks to the nutritional value, advantages for human diets and edibleness as other shellfish such as shrimp, clam, lobster, scallop, abalone and crab, mussel is in growing value. It is valuable to exploit it. This study of PEF method to extract protein from mussel is important to utilize the mussel meat. PEF, with advantages of non-thermal performance, speediness, efficiency, low power and low pollution, is currently used for non-thermal pasteurization of food and extraction of value components from different natural sources. The results of this study are helpful to the further research of PEF method of protein extraction of mussel and, as such, are of practical significance.