As one of the most important direction of non-contact 3D shape measuring method, optical technology has been widely applied in the fields of industrial production, automatic detection, quality control, machine vision, cultural preservation, and so on. With the advent and development of high performance devices such as DLP (Digital Light Processing) projector and CCD camera, digital fringe pattern projection techniques have become a rapidly developing area. However, when four-step phase-shifting algorithm is used to calculate the wrapped phase, the intensity fluctuation of the captured fringe patterns may affect the accuracy of the final measurement results. This paper presents a novel method to eliminate the intensity fluctuation of the captured fringe patterns by using EMD (Empirical Mode Decomposition) algorithm. Four fringe patterns which have pi/2 phase shift in between need to be captured for four-step phase-shifting algorithm. In order to eliminate the intensity fluctuation between fringe patterns, every fringe pattern is decomposed into a number of IMFs (Intrinsic Mode Function) by using EMD. After being processed, the four fringe patterns have the same background light intensity and contrast. Both simulated and experimental data are tested to verify the validity of the proposed method. The results show that the intensity fluctuation between fringe patterns can be effectively eliminated to give accurate phase data.