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Aquatic protein hydrolysates have many biological activities, but the off-flavor seriously decreases their commercial acceptability. Therefore, it is important to invest in finding an effective deodorization of aquatic hydrolysates that do not affect activities. In this study, ethanol pretreatment of mussel was applied to establish a new method to deodorize the blue mussel (Mytilus edulis L.) hydrolysates. LC-MS and GC–MS analysis results showed that 87.34% of fatty acids, 83.94% of aldehydes, most volatile flavor compounds including aldehydes, ketones, alcohols, acids, and hydrocarbons were decreased after ethanol pretreatment. Besides, it was found that the enzymatic hydrolysates of mussel with or without ethanol pretreatment showed high osteogenic activity, which induced an increase of 33.65 ± 4.36% and 31.77 ± 5.45% in MC3T3-E1 cell growth. These results suggest that ethanol pretreatment has beneficial potential for improving the flavor aspects of blue mussel peptides which may have the potential to stimulate bone regeneration and formation.