Citrus greening is a severe disease significantly affecting citrus production in the United States because the disease is not curable with currently available technologies. For this reason, monitoring citrus disease in orchards is critical to eradicate and replace infected trees before the spread of the disease. In this study, the canopy shape and vegetation indices of infected and healthy orange trees were compared to better understand their significant characteristics using unmanned aerial vehicle (UAV)-based multispectral images. Individual citrus trees were identified using thresholding and morphological filtering. The UAV-based phenotypes of each tree, such as tree height, crown diameter, and canopy volume, were calculated and evaluated with the corresponding ground measurements. The vegetation indices of infected and healthy trees were also compared to investigate their spectral differences. The results showed that correlation coefficients of tree height and crown diameter between the UAV-based and ground measurements were 0.7 and 0.8, respectively. The UAV-based canopy volume was also highly correlated with the ground measurements (R2 > 0.9). Four vegetation indices—normalized difference vegetation index (NDVI), normalized difference RedEdge index (NDRE), modified soil adjusted vegetation index (MSAVI), and chlorophyll index (CI)—were significantly higher in healthy trees than diseased trees. The RedEdge-related vegetation indices showed more capability for citrus disease monitoring. Additionally, the experimental results showed that the UAV-based flush ratio and canopy volume can be valuable indicators to differentiate trees with citrus greening disease.