A fin lifting system of a comprehensive marine science research ship comprises a deep well, a lifting device, a fin instrument chamber, a underwater load balance locking device, an auxiliary lifting device, an emergency locking device, a safety protection device, a hydraulic electric control system and a sound-light alarming system, which are all installed in a ship body. The fin instrument chamber is used for installing reliable probe devices, and connected with the lifting device by a steel rope to control up-and-down motion of the fin instrument chamber in the deep well of the ship body; the fin instrument chamber is underwater for the long term, the underwater load balance locking device is responsible for compressing the fin instrument chamber with the ship body tightly, so that the fin instrument chamber is protected from being relatively crashed with the ship body; when the underwater load balance device is ineffective, the fin instrument chamber can be lifted to be above a waterline and locked by the emergency locking device to prevent wobble in the ship body; the auxiliary lifting device is used for lifting the instrument devices in the fin instrument chamber for convenient maintenance. Other accessory devices include a cable bracket, a vertical ladder, a lighting tool and the like.