To exploit the by-products of tuna processing and make full use of the nutrients from tuna fish oil, microcapsules were prepared by spray-drying and freeze-drying with chitosan as shell material and tuna fish oil as core material. The effects of two preparation methods on the quality of microcapsules made were compared. The results showed that the embedding rates of spray-dried and freeze-dried microcapsules were 77.26% and 63.86% respectively, but the freeze-dried microcapsules can better protect the fatty acids of fish oil. A total of 43 volatile components in spray-dried microcapsules were identified, and ketones were the most, reaching 33.01%. There were a total of 24 volatile components in freeze-dried microcapsules, mainly esters, reaching 52.29%. No typical fishy odor substances were detected, which may be due to the low temperature in the freeze-drying process that inhibited the oxidation of polyunsaturated fatty acids and could cover up the bad flavor of fish oil. During storage, compared with fish oil, the growth rate of peroxide value of the two kinds of fish oil microcapsules was significantly reduced (P<0.05). The retention rates of DHA + EPA were 82.22% and 85.25% respectively after 7 days, and two preparation methods had little effect on retention rate of DHA + EPA (P>0.05). The research showed that the two kinds of preparation methods for fish oil microcapsules had certain effect on delaying the oxidation of fish oil and masking bad flavors, and were of reference significance for the preparation of fish oil microcapsules.