Abstract: A kind of double time domain Fourier transform is proposed. By cuting the time varied intensity of two phase shift cycle into many pieces of time varied intensity with one phase shift cycle, then separats phase shift frequency and disturbance frequency by performing Forier transform two times. Both numerical simulation and experiment result s show this algorithm simplifies the phase shifting system, deduces the data acquision and improved the ability of noise resistence, it needs no manual intervention while performing this algorithm and has the property of automation.