In color-encoded phase measurement profilometry, the obtained phase shifting fringe pattern is distorted caused by the color crosstalk and uneven intensity responses among multiple optical channels in the optoelectronic device and other factors. Consequently, large phase errors arise when phases are solved by the classical phase technique. A two-step correction method is proposed by analyzing the characteristics of the fringe patterns in the red, green, and blue channels obtained by the color imaging device with a mathematical model of color-encoded fringe patterns. The first step is to normalize the intensities of the images in the three channels with their mean value and standard deviation. In the second step, the actual phase shifts after distortion are searched with the probability density function curve, and the influence of inaccurate phase shift on the measurement result is reduced. The propsoed method does not need to pre-correct the coupling coefficients and phase shift offsets of the system, and it can achieve simple and fast phase error compensation. Simulation and experimental results verify the effectiveness of the proposed method.