In the food industry, syrups containing a high concentration of sugar used for fruit preservation is abundantly discharged as a food processing waste and disposed by incineration, resulting in the rise of the manufacturing cost and environmental pollution. This study demonstrates how waste syrup can be utilized as carbon source for production of docosahexaenoic acid (DHA) and astaxanthin by the thraustochytrid strain, Aurantiochytrium sp. KH105. The strain could grow in culture medium containing 3-50% waste syrup, and the maximum yields of DHA and astaxanthin were 207.6 mg/L (at 50%) and 1.1 mg/L (at 25%), respectively. After the optimization of culture medium composition by response surface method, DHA and astaxanthin yields increased by 2.1 and 1.5 fold, respectively. When the waste syrup was treated with activated charcoal, citrate concentration in the syrup was reduced and the astaxanthin yield increased by 2.3 fold. This study shows that the waste syrup can be effectively used for the functional lipid production by the thraustochytrid.