There is more and more research on the application of UAV in animal surveys, but there is no effective automatic image processing method, which makes the work of visual interpretation heavy. In order to quickly and accurately count the number of large herbivores in the source area of the Three Rivers, two UAVs were used to collect images from seven sites. Initially, the UAV image is grayed to reduce the matrix dimension and retain the gradient information, which greatly improves the operation speed. Secondly, the image is filtered by Gauss filter, which transforms the data into energy and eliminates the noise belonging to the low-energy part. Thirdly, threshold processing is carried out to get the binary image. Then the morphological characteristics of animal husbandry in the sample are used to produce the shape. The state operation first eliminates the interference of small objects as much as possible without deleting livestock by mistake, and then excludes small black holes by closed operation to connect the same object without repeated counting. Finally, the contour is retrieved from the binary image and the number of detected contours is returned. Thus, the number and spatial distribution of the main livestock species are automatically obtained. Comparing manual counting with automatic counting, the relative error is between 3.1% and 6.5%, which can be reached in most cases. The average time of image processing and counting is less than 3 seconds after automatic image processing by computer. The automatic processing method of UAV image can provide an effective and reliable technical way for large-scale investigation of Tibetan sheep, yaks, Tibetan wild ass and Tibetan antelope in the future.