The invention discloses an online analysis system of a ship exhaust emission. The online analysis system of the ship exhaust emission comprises a flue gas sampling unit, a flue gas pretreatment device, a flue gas analysis system, a flue gas parameter measuring system, an automatic blowback control system, a data acquisition system (DAS), a smoke monitoring system, a flue, a gas testing room and an analysis instrument cabinet, wherein the flue gas sampling unit comprises a sampling probe, a smokometer, a flowmeter, a moisture tester, a pressure sensor and a temperature sensor; the flue gas pretreatment device comprises a sample gas pretreatment unit, calibration equipment and a purging unit; the flue gas sampling unit is arranged in the flue, and connected with the analysis instrument cabinet through a cable; the flue gas pretreatment device and the flue gas analysis system are both mounted in the analysis instrument cabinet. With the adoption of the online analysis system of the ship exhaust emission disclosed by the invention, real-time, on-line and continuous detection of a variety of pollutants in flue gases can be carried out, a gas chamber can be prevented from corrosion damage and pollution, and a gas pipeline can be prevented from blockage; furthermore, the performances are stable and reliable, and the maintenance workload is small.