The invention relates to a manned submersible emergency navigation controller installed in a manned submersible manned cabin and a manned cabin external electronic cabin, and forming a manned submersible navigation control system together with a main navigation control system. A core circuit of the controller is composed of an embedded controller, an A/D, a D/A, an operational amplifier, etc. A circuit board in the manned cabin is used for acquiring and processing signals of a joystick on a control box; a circuit board in the electronic cabin is used for analyzing control instructions and outputting propeller control signals; and two circuits communicate with each other through a cabin penetration watertight cable. When the main navigation control system of a submersible breaks down, the emergency navigation controller can be switched to perform emergency navigation control on the submersible, thereby guaranteeing a basic navigation motion capability of the submersible and realizing safe course reversal.