Based on fiber Bragg grating and Fourier heat conduction equation, a method of water-heat is used to measure the thermal diffusivity of composite cylindrical structure, with theoretical analysis and experimental research represented. When the temperature of fluid in cylindrical structure rises, the initial low-temperature equilibrium state of cylindrical structure transits to high-temperature equilibrium state, its internal fluid heat is transmitted from inside to outside, the structure exhibits different temperature characteristics due to the thermal resistance. According to this principle, the center wavelength with temperature function relationship is obtained by experiment, followed to get the relationship between the center wavelength and time functions, the cylindrical structure temperature distribution function is conclude. Based on the Fourier one dimensional heat conduction equations and boundary conditions, the structural thermal diffusivity can be obtained. Result shows that the cylindrical structure thermal diffusion coefficient in heating and cooling process is consistent, which proves the feasibility of the measurement program. Water-heat balance method is simple, stable, operable, which provides a novel and feasible method for such cylindrical structure of the thermal diffusivity measurement.