To improve the stability and solubility of Cornus officinalis flavonoid (COF), spray drying (SD), freeze-drying (FD), and microwave freeze drying (MFD) were used to encapsulate COF using whey isolate protein (WPI) and gum arabic as wall materials. The characterization of COF microparticles was performed with encapsulation efficiency (EE), particle size, morphology, antioxidant activity, structure, thermal stability, color, stability during storage, and in vitro solubility. The results showed that COF was successfully encapsulated in the wall material with an EE between 78.86% and 91.11%. The freeze-dried microparticles had the highest EE (91.11%) and the lowest particle size (12.42±16.73µm). However, the particle size of COF microparticles of SD and MFD was relatively large. The 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging capacity of the microparticles obtained from SD (89.36mgVc /g) was higher than that of MFD (85.67mgVc /g), but the drying time and energy consumption of microparticles dried by SD and MFD were lower than those of FD. Furthermore, the spray-dried COF microparticles had higher stability compared to FD and MFD when stored at 4°C for 30 days. In addition, the dissolution of COF microparticles prepared by SD and MFD was 55.64% and 57.35%, respectively, in simulated intestinal fluids, which was lower than that of FD (64.47%). Therefore, the application of microencapsulation technology showed significant advantages in improving the stability and solubility of COF, and the SD can be used for the preparation of microparticles considering energy cost and quality. PRACTICAL APPLICATION: COF is an important bioactive ingredient, but its poor stability and water solubility decreases its pharmacological value. COF microparticles can improve the stability of COF, enhance the slow-release effect, and expand its application in the food field. The drying method will affect the properties of COF microparticles. Thus, the structures and properties analysis of COF microparticles by different drying methods can provide a reference basis for the preparation and application of COF microparticles.