The invention relates to a phase unwrapping method based on colored phase shift stripe secondary encoding. The method comprises the following steps of: firstly generating a colored phase shift stripe, projecting the colored phase shift stripe onto the surface of a measured object, collecting a deformation phase shift stripe graph, transmitting deformation phase shift stripe image data to a computer, utilizing Matlab software to divide the deformation phase shift stripe graph into three phase shift gray level images, solving the phase distribution of the deformation phase shift stripe graph, further solving the wrapping phase of the object, then utilizing the color and luminous intensity alternating rule to realize a first time of colored encoding, carrying out secondary encoding on the basis of the first time of encoding in the sequence of red, green and blue, stipulating that three colored encoding stripes generated by the colored phase shift stripe is a cycle of a stripe graph, encoding the stripes with a two-digit number, wherein the cycle, in which the deformation stripe falls, is represented by encoding of respective regions, and adopting a method of respectively counting the numbers of stripes of each color to determine the cycle number of the stripe in the graph and solve the true phase, thereby reducing the data matching error and promoting the unwrapping speed.