Disclosed are a method and system for precise height positioning based on global navigation satellite system (GNSS). A precise height positioning method may include determining an orthometric height based on a barometric pressure and a temperature of a region where an unmanned aerial vehicle is located, determining a geoid height in accordance with GNSS positioning information of the unmanned aerial vehicle, and determining a final altitude based on a difference between an ellipsoidal height in accordance with the orthometric height and the geoid height and an ellipsoidal height included in the GNSS positioning information.