The invention discloses a tower for observing an atmospheric boundary layer underlayer structure and air-sea flux exchange of an island reef. In combination with the main body structure design of the tower, the instrument mounting structure design and design and implementation of a data observing system, a multisource sensor can be mounted on the observing tower to realize gradient observation of the temperature, the humidity, the air pressure, the wind speed and the wind direction of the bottom layer of a 0-20 meter atmospheric boundary layer underlayer and observation of sensible heat flux, latent heat flux, momentum flux and carbon dioxide flux of an air-sea interface within the radius range of 2,200 meters in the upwind direction. By means of the structure and data acquisition system design, the tower for observing the atmospheric boundary layer underlayer structure and air-sea flux exchange of the island reef has the characteristics that the observation parameters are diversified, corrosion resistance is realized, the system is convenient to maintain in the severe weather process, the observation cost is low and the like, a new means can be provided for observation of boundary layer structures and air-sea flux of the South China Sea, and meanwhile, a foundation is laid for next synchronous networking observation of multiple island reefs.