A high-carrying-capacity through rail transit system comprises a main passage, operating compartments, an exit and entrance passage, rails, and a station. The operating compartments are independent small compartments (200). The rails are laid in the main passage (100) and are power rails that keep moving at a constant speed. The independent small compartments are placed at corresponding positions on the power rails, and the power rails drive the independent small compartments to advance at a constant speed. The station (400) is connected to the main passage having the power rails through the exit and entrance passage (300). One end of the exit and entrance passage is connected with the station and the other end of the exit and entrance passage is connected with the main passage to form a communicated structure. A connecting device is provided at the top of each independent small compartment, and the connecting device and a connecting structure arranged above the exit and entrance passage are butt-joined to complete rail change. The system adopts the independent small compartment mode, so every passenger has a seat and the through purpose is realized; stable and continuous kinetic energy for advancing are provided; and the independent small compartments have no relative displacement and can reach a high speed under high density.