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This invention belongs to the field of functional food processing technology, specifically relating to a method for improving the flavor of a chlorophyll-deficient Chlorella proteoglycan mutant. The method includes the following steps: S1, obtaining a Chlorella proteoglycan mutant strain; S2, centrifuging the Chlorella proteoglycan mutant strain and collecting the algal sludge, then pulverizing the collected algal sludge and dispersing it in water to obtain an algal powder suspension, then adding a compound enzyme to the algal powder suspension, and inactivating the enzyme after the reaction; S3, cooling the system to room temperature, adding glucose and stirring to dissolve, sterilizing, inoculating with a compound bacterial strain and fermenting, and sterilizing again after fermentation; S4, cooling the fermented system to room temperature, then adding β-cyclodextrin and stirring, and drying the system after stirring to obtain the algal protein product. This invention employs a synergistic process of compound enzymatic hydrolysis, compound bacterial fermentation, and β-cyclodextrin encapsulation to remove the off-flavor of the mutant algae from the source, significantly improving the flavor and enhancing the product's storage stability.