A novel process was developed for encapsulation of astaxanthin from Phaffia rhodozyma. The yeast cells were disrupted by glass beads and the high shearing force partially emulsified the astaxanthin in aqueous phase. The enzymolysis method was then adopted to prepare the yeast extract for a full use of the cells. The gelatin and porous starch were used to microencapsulate the emulsified astaxanthin. Under optimized conditions, the recovery of amino nitrogen and solid reached 3.68 ± 0.32% and 49.22 ± 2.34%, respectively. The microencapsulation conditions were optimized through orthogonal experiment and the encapsulation efficiency, loading astaxanthin, and amino-nitrogen reached 88.56%, 1.55 mg/g, and 1.35 ± 0.14%, respectively. The water solubility of microcapsules reached 81.5 ± 0.35%. Color and storage stability analysis showed that microencapsulation of astaxanthin possessed higher thermal stability. The results demonstrated that the established process was effective and practical.