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A method to determine the optical parameters of polymer thin film by use of the transmission spectrum is proposed, with the improved simulated annealing algorithm developed to perform its inverse calculation. A special phenomenon due to the almost equal refractive index between film and substrate, that is, the small waves on spectrum curves which make the information of film thickness losing, has been discussed in detail. Based on the tested transmission spectrums of polymer optical thin films fabricated on K9 glass substrates, the dispersion curve of refractive index in visible band is figured out. Its calculated refractive index in the wavelength of 1547 nm is 1.3933, with the accuracy higher than 0.58% by comparing with the one measured by traditional coupled prism method. The analyzed result shows that the improved algorithm works well, by which the calculated optical parameters can converge to the right values.