Aiming at the problem that the traditional three-frequency three-step phase shifting algorithm in structured light three-dimensional measurement needed to project too many fringe patterns and has low efficiency, the modified three-frequency three-step phase shifting algorithm was proposed. The proposed algorithm and traditional one both required sinusoidal fringe patterns of three frequencies, but the number of fringe patterns was reduced to 5, that was, 3 fringe patterns of the highest frequency, and one for each of the other two frequencies. Compared with 9 fringe patterns of the traditional algorithm, the projection and capture efficiency was increased by 44.44%. The principle of the proposed algorithm was derived. Three fringe patterns of the highest frequency were used to directly obtain the wrapped phase, and the other two fringe patterns were used to unwrap the phase. In theory, the proposed algorithm owned the same accuracy as the traditional one. Finally, four sets of experiments were conducted to verify the reconstruction accuracy of the algorithm, the reconstruction ability of complex discontinuous models, the reconstruction stability in different illuminations, and the reconstruction ability of color objects. The experimental results prove that the algorithm can effectively improve the measurement speed while maintaining the accuracy and adaptability consistent with the traditional three-frequency three-step phase shifting algorithm.