Owing to the presence of aerosol in the troposphere(below 12km), traditional method which uses Rayleigh scattering spectrum to measure the atmosphere temperature has certain limitations. This paper uses a Fourier analysis method to proceed transmission curve produced by atmospheric backscattering spectrum through the iodine cell, considering the influence of the aerosol. This method can obtain the temperature profile of the troposphere under the condition of different height and different backscattering ratio.