The transparent electrode thin film of ITO is widely used to implement the touch function of flat panel display(FPD). Its physical thickness has a great impact on touch panel operation, therefore it is very important to measure the thickness of transparent electrode film. The frequency domain analysis algorithm has been used to measure film thickness. However, it is difficult to measure the very thin film. A new algorithm is proposed to measure the film thickness ranged from 20 nm to 150 nm. This algorithm aims to get the precision phase distribution due to multiple reflection of film. The experimental results show that the thickness of the measured transparent electrode film is 90-104 nm, which illustrates that there is no difference from the calibration value. This result proves that the new algorithm can be used to measure the very thin film of ITO within 100 nm.