Citrus fruit, one of the most important economic crops, is playing an important role in the industrial development of modern agriculture in rural China. However, the management mode of most orchards in China is currently undeveloped and extensive, particularly with high dependence on labor force, as well as insufficient scientific and technological support. In recent years, the Unmanned Aerial Vehicle (UAV) monitoring technology has become a significant way to quickly extract the structural parameters in the growth of field crops at the park scale, due to its flexibility, low cost, and high resolution imaging. This study aims to construct a monitoring system for the citrus canopy structure and nutrition information using the UAV digital and multi-spectral remote sensing, to get he with the single tree segmentation. The UAV digital images and watershed algorithm were used to segment the structural dataset of citrus canopy, and then the canopy height model of citrus trees was established to extract the plant height using digital surface module. Structural parameters were also calculated, such as the number of citrus trees, and canopy projection area at the park scale. In addition, the UAV multispectral images were used to obtain eight common vegetation indexes, thereby to predict the nitrogen content of canopy in the citrus trees. The whole subset analysis was used to screen the sensitive vegetation index for the nitrogen content of canopy in the citrus trees. The inversion model of canopy nitrogen was constructed using the multiple linear regression. The remote sensing mapping was carried out to estimate the nitrogen content of citrus canopy in park scale. The results showed that: 1) Since the planting density of fruit trees was low in the experimental area, there was a certain distance between trees that can be clearly distinguished. The watershed image processing was selected to segment the single tree of height model for a citrus canopy. The overall identification accuracy, recall rate, and average F value of the fruit trees were above 93%, 95%, and 96.52%, respectively, indicating that the model was well suitable to monitor the number of fruit trees in the park. 2) The canopy structure parameters of individual fruit trees were obtained in the individual tree segmentation. There was a strong correlation between the plant height of citrus trees extracted by the canopy height model and the measured value, where the R2=0.87, and RMSE=31.9 cm. 3) Using the watershed segmentation, the extracted projection area of crown width per plant achieved a high correlation with the artificial sketching area. The coefficient of determination was more than 0.93 in most cases, except that of orchard A lower than 0.78 in December. Meanwhile, the extraction accuracy of the model depended greatly on the single tree segmentation. 4) In full subset analysis, the sensitive vegetation indexes were selected to determine the nitrogen content of citrus canopy, including the Normalized Difference Vegetation Index (NDVI), Green Normalized Difference Vegetation Index (GNDVI), and Structure Insensitive Pigment Index (SIPI), where the R2 and RMSE of the model were 0.82 and 0.22%, respectively. The data demonstrated that the nitrogen content of most fruit trees in orchard B was in the suitable range, while there was excessive application of nitrogen fertilizer in orchard A. Therefore, the UAV technology can greatly contribute to extract the physical and chemical parameters of citrus canopy, further to improve the level of accurate management of citrus on the large-scale orchard.