To mitigate the fishy odor and enhance the quality of Porphyra yezoensis, enzymatic pretreatment combined with microencapsulation was applied. Microcapsules were prepared by spray drying using β-cyclodextrin, soybean protein, and maltodextrin as composite wall materials. The effect of microencapsulation on the volatile flavor components of P. yezoensis was investigated along with the physicochemical properties and structural characteristics of the microcapsules. The optimal process conditions were determined as follows: inlet temperature of 170 ℃, homogenization rate of 13000 r/min, and core-to-wall ratio of 1:50. Under these conditions, the encapsulation efficiency was 81.26%, and the microcapsules exhibited a particle size range of 150–260 nm, a moisture content of 4.76%, a solubility above 90%, and an angle of repose of 42.18°. Structural characterization using Fourier transform infrared spectroscopy(FTIR) and X-ray diffraction(XRD) confirmed the successful embedding of the core material within the wall matrix. Analysis via headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry(HS-SPME-GC-MS) and relative odor activity value(ROAV) demonstrated that the total number of flavor compounds decreased by 38 after deodorization. The concentrations of key odor-causing substances, such as β-cyclocitral, hexanal, and 1-octen-3-ol, were significantly reduced or became undetectable, while those of aldehydes and pyrazines responsible for floral, fruity, and roasted nut aromas increased markedly, becoming the dominant flavor compounds in the microcapsules. These results indicate that microencapsulation can effectively mitigate the fishy odor of both untreated and enzymatically pretreated P. yezoensis, providing a viable method and technical reference for the value-added processing and flavor control of laver products.