The casein-pectin conjugate was prepared by Maillard reaction, and the effects of pectin on the structural and functional properties of casein was investigated. The optimum process for casein-pectin conjugate was determined by combining response surfaces with single factors taking the grafting degree and browning index as the response values. Flaxseed oil microencapsulation was prepared using casein-pectin conjugate as wall materials. The results showed the optimum process conditions were casein-pectin mass ratio 3∶1, heating time 1.5h, and heating temperature 90℃. The grafting degree of casein-pectin conjugate were 37.06%±0.80% and the browning index was 1.05±0.014. The determination results of secondary structure showed that the α-helixes, β-sheets, and β-turns contents of casein-pectin conjugate was decreased by 26.39%, 9.21%, and 2.23%, respectively, while the random curl content was increased by 12.43%, compared with casein. The functional properties (solubility, emulsification, thermal stability and antioxidant activity) of casein-pectin conjugate were significantly improved compared with casein. Flaxseed oil microencapsulation was prepared by spray drying using casein-pectin conjugate as the wall material and flaxseed oil as the core material. The results showed that the maximum encapsulation efficiency (77.06%±0.98%) was reached at mass ratio of 1∶1 between casein-pectin conjugate and flaxseed oil, and the microencapsulation had a complete spherical structure without fragmentation. In addition, the peroxidation value of free flaxseed oil was (14.70±0.51) meq/kg after stored at 25℃ for 28d, the peroxidation value microencapsulated flaxseed oil was only (3.82±0.07) meq/kg, indicating that the antioxidant activity of flaxseed oil was significantly improved by casein-pectin conjugate. This study aimed to provide a scientific basis for the application of casein in food industry.