There is a growing interest in using polymethoxyflavones (PMFs, a unique class of flavonoids found in citrus fruits) as nutraceuticals because of their multiple health-promoting effects. However, their application in food system is restricted by their poor water solubility and emulsion-based delivery systems are potential means to increase food applicability of PMFs. Herein, the properties and encapsulation efficiency of emulsion and re-dispersible emulsion containing PMFs were determined based on citrus oil and corn oil.Emulsions consisting of maltodextrin (25 wt%) and citrus pectin (1 wt%) in oil phase, citrus oil or corn oil (5 wt%) in water phase were produced and spray dried at different outlet temperatures (110 °C, 130 °C, 150 °C, 170 °C, 190 °C) after homogenization (700 MPa). A series of analytical methods were used to characterize these emulsion systems.It was shown from the SEM that the microcapsules of citrus oil presented as spheres with concave-convex surface while those of corn oil presented with smooth surface. The wrinkle surface observed in citrus oil capsule might be attributed that high inlet temperature causes the rapid evaporation of citrus oil, and the smooth surface of corn oil capsule were due to the better structural integrity which was resistant to the mechanical stress during spray drying. As the dryer outlet temperature increased, the degree of particle breakage raised and water content, particle size, flavor compounds and encapsulation efficiency of PMFs in powders reduced. PMFs retention was higher in citrus oil powders than that in corn oil ones at the same temperature, which due to the citrus oil has the better solubility of PMFs and the less particle breakage. Moreover, the citrus oil powder had better water-dispersibility and pleasant flavors than corn oil one.The encapsulation efficiency of PMFs was optimal by using the citrus oil as carrier oil, the maltodextrin as wall material and the 150 °C as the outlet air temperature. The results may facilitate the rational design of natural delivery systems to prepare PMFs-enriched functional foods and dietary supplements.The encapsulation efficiency of PMFs was optimal by using the citrus oil as carrier oil, the maltodextrin as wall material and the 150 °C as the outlet air temperature. The results may facilitate the rational design of natural delivery systems to prepare PMFs-enriched functional foods and dietary supplements.