Calibration is to transform the two-dimensional (2D) phase information to the height in fringe projection three-dimensional (3D) measurement. An equi-phase coordinate method based on two reference planes for calibrating fringe projection system is proposed. The surface height is calculated by a linear interpolation using the coordinates where have the identical phase value of the object and the two reference planes, instead of using the absolute phase obtained by subtracting the phase of object from the reference plane in the same coordinate conventionally and building the function of the absolute phase and height, which is called equi-coordinate phase method. The proposed method can handle phase-to-height conversion and non-sinusoidal error caused by nonlinear respondence of the fringe projection system in one go. Theoretical and experimental analysis is given to prove the validity of the proposed calibration method. Results indicate that the root mean square (RMS) error produced by equi-phase coordinate method is less half of the equi-coordinate phase approach when the primary error source is from the non-sinusoidal fringe patterns.