The present invention discloses a system and method for synchronously collecting shipboard videos based on an MEMS inertial sensor and a camera. The system comprises: an MEMS inertial sensor mounted on a camera in a strap-down mode, wherein the MEMS inertial sensor can collect attitude data of the camera in real time and periodically send synchronization trigger signals for performing exposure control on the camera; a camera, wherein the camera performs exposure shooting according to the synchronization trigger signals, to collect corresponding video data; and an upper computer which is connected to the MEMS inertial sensor and the camera respectively, wherein the upper computer can perform parameter setting on the MEMS inertial sensor and the camera and synchronously store the attitude data and video data. The system disclosed by the present invention can use synchronization trigger signals sent out by an inertial sensor to control the time of exposure of a camera, to synchronously collect and store inertial sensor data and video data, thereby further providing a data guarantee for the electronic image stabilization algorithm for shipboard videos.