The invention relates to a plant protection unmanned plane operation system for fruit trees based on the geographic information fusion technology, and belongs to the field of plant protection unmanned plane operation systems. The system mainly comprises surveying and mapping equipment, and the surveying and mapping equipment comprises an RTK surveying and mapping device and a dividing ruler. The RTK surveying and mapping device can achieve the surveying and mapping of the geographic positions of a fruit tree and a barrier which is fixed for a long time. The dividing ruler can achieve the surveying and mapping of the morphological parameters of the fruit tree. The system also comprises a plant protection database, and the plant protection database carries out the database building arrangement of the geographic positions of the fruit tree and the barrier which is fixed for a long time, the morphological parameters of the fruit tree and the plant protection operation information of the plant tree, wherein the geographic positions of the fruit tree and the barrier and the morphological parameters of the fruit tree are collected by the surveying and mapping equipment. The system also comprises an atomizing-type unmanned plane, and the atomizing-type unmanned plane forms an exclusive operation flight route of each land parcel according to the information of the plant protection database, and carries out the plant protection operation according to the operation flight routes. The beneficial effects of the invention are that the system achieves the precise operation, reduces the repeated spraying and spraying leakage, reduces the consumption of farm chemicals, is safe and environment friendly, and improves the operation efficiency.