The present invention provides a method and system for real-time high-precision positioning in the deep sea. The present invention, based on a ray theory model, uses an azimuth angle, a transmission delay, a deep-sea vehicle depth and a depth of an acoustic transducer of a water surface monitoring platform as an eigenray emergence angle, an eigenray transmission time, eigenray emergence depth and an eigenray end point depth respectively, quickly calculates an eigenray that connects the water surface monitoring platform with the deep-sea vehicle, accurately calculates a position of the deep-sea vehicle relative to the water surface monitoring platform, and converts the position into absolute position information of the deep-sea vehicle through the latitude and longitude of the water surface monitoring platform, thereby achieving real-time high-precision positioning.