The invention provides a protein separator for live fish transportation which is different from a traditional protein separator. The invention pumps waste water in a fish container and preprocessed cooling water into the separator body for confluence and mutual disturbance through two sets of ejectors connected in parallel (meanwhile, the ejectors inhale pure oxygen gas to fully blend with ejecting water flow according to the working principle of Venturi) and blend again with micro bubbles released from a dissolved oxygen aeration micropore pipe component, then rising turbulent water flow is generated after combined action. During the motor process of water flow from bottom to top, a large number of micro bubbles constantly coacervate with protein, fiber, suspended particle and jelly and the like in water body to become larger and larger and generate air floating effect, ensuring soiling in the water body to rise in the form of concentrated bubbles to the pipe and be outputted by a drainage tube, thus organic hazardous substances in the water body and the like are effectively separated and wiped out; meanwhile clean water separated from injurants such as protein and the like refluxes to the fish container through a effluent drainage tube which is connected with a drain pipe, thereby realizing the purpose of the invention.