The invention relates to monitoring system and a monitoring method for an automatically operated unmanned aerial vehicle for plant protection. The monitoring system for the automatically operated unmanned aerial vehicle for plant protection comprises a depth data acquisition unit, a GIS (geographic information system) processing unit and an automatic control unit. Through the depth data acquisition unit and a color data acquisition unit, depth information and color information of farmlands are acquired respectively. Through the GIS processing unit, the depth information and the color information of the farmlands are processed and analyzed to obtain information of areas with planted crops. Through the automatic control unit, the unmanned aerial vehicle is automatically controlled to performplant protection on crops in the areas without missing precisely.