Rutin possesses a wide range of application prospects with various bioactivities. However, its bitter and water-insoluble properties restrict its application in the field of functional foods. A new complex of rutin and chitooligosaccharide (Rutin-COS) was prepared via spray-drying method (100 °C, 1 L/h) and freeze-drying method (−80 °C, 24 h), respectively. The water solubility, bitterness, antioxidant and antibacterial activities of Rutin-COS were evaluated, and the complexation of Rutin-COS was characterized by SEM, 1H-NMR and ROESY. Compared to freeze-drying method, spray-drying method was more effective for preparing stable Rutin-COS complex. The spray-dried Rutin-COS showed increased water solubility, weakened bitterness, enhanced antioxidant and antibacterial activity compared to rutin. The Rutin-COS complex was demonstrated to be formed through hydrogen bonds between the A, B rings of rutin and COS.