The invention discloses a fluorescent labeling method for living organisms having cell membrane structures. The fluorescent labeling method comprises the following steps: co-culturing choline analogue containing azide group and a living organism having a cell membrane structure and acquiring choline analogue modified living organism after metabolism; and marking the choline analogue modified living organism by adopting DBCO (dibenzocyclooctyne) group modified fluorescent marker through the click chemical reaction and enabling the fluorescent marker to be labeled on the surface of the cell membrane of the living organism. According to the fluorescent labeling method for the living organism having the cell membrane structure, the choline analogue containing azide group is adopted to modify the living organism, and the method has little influence on the activity of the living organism; and the fluorescent labeling method adopts a one-step method for marking, compared with the two-step method, the one-step method can be operated simply and has high efficiency.