A deep-sea low-cost long-endurance collaborative navigation and positioning system. A shore-based monitoring center transmits a route planning solution to a wave glider. The wave glider follows an underwater vehicle to travel and feeds back state information of the wave glider and state information of the underwater vehicle to the shore-based monitoring center in real time. The shore-based monitoring center adjusts the route planning solution according to the state information in real time. The wave glider and the underwater vehicle are respectively equipped with an underwater acoustic communication machine. The wave glider obtains self location and time information through a satellite and transmits the location and time information to the underwater vehicle in an underwater acoustic communication manner, then the underwater vehicle calculates a horizontal distance between the underwater vehicle and the wave glider to assist a microelectromechanical system (MEMS) sensor of the underwater vehicle in navigation and positioning.