It is important to eliminate the fishy odor and improve the aroma quality of seafood. In this study, the Saccharina japonica (S. japonica) seedling, which is a new food material, was investigated for the effects of fermentation with Saccharomyces cerevisiae (S. cerevisiae) through sensory evaluation, GC–MS, and odor activity value (OAV) analysis. GC–MS analysis revealed the presence of 43 volatile compounds in the unfermented S. japonica seedling, with 1-octen-3-ol, hexanal, and trans-2,4-decadienal identified as the main contributors to its fishy odor. After fermentation with S. cerevisiae, 26 volatile compounds were identified in the S. japonica seedling. Notably, the major malodorous fish compounds, including 1-octen-3-ol, hexanal and trans-2,4-decadienal, were no longer present. The results indicate that fermentation with S. cerevisiae is an effective method for removing fishy malodor compounds and enhancing the volatile components with fruity, sweet, green, and floral notes in the Saccharina japonica seedling. This process facilitates the elimination of fishy malodor and enhance the fruity, sweet, green, and floral notes of S. japonica seeding and other seaweeds.