To evaluate oxidative stability of microencapsulated oils rich in polyunsaturated fatty acids, the change of peroxide value (POV) during storage was investigated. Microencapsulated oils were prepared by spray drying emulsions containing oils rich in docosahexaenoic acid or arachidonic acid, caseinate, modified starch and maltodextrin. Results showed that oxidative stability and initial POV of oils, packing and storage temperature all affected markedly oxidative stability of microencapsulated oils. It is necessary for obtaining stable microencapsulated oils to choose oils of high oxidative stability and low initial POV, reduce oxygen content in wrapper and lower storage temperature. Basing on our findings, six stages of the oxidation of microencapsulated oils were suggested as compared with three stages of the oxidation of oils. It is very important for the oxidative stability and shelf-life to extend the first and the forth stages, shorten the second and the third stages, and avoid the fifth and the sixth stages during oxidation of microencapsulated oils.