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Phase modulated object height information is get by phase shift technology or Fourier transformation technology in the PMP measurement system, and then get continuous phase by phase demodulation and phase unwrapping technology, and get object height information based on system height formula. In theory, telecentric beam path projector lens center and CCD incidence diaphragm center are located in the common vertical plane, and their light axis are located in the common horizontal plane, and then exact system parameters are get. But it is impossible to come true this demand in fact. So in this paper, calibrate object height and optimize structure parameters in a general system by the least square interactive method and genetic algorithm, in which selected real-coded Genetic algorithm, right population size, adaptive fitness function, crossover operator and mutation operator, and then realized spatial identification. Compared with the traditional least square interactive method, experimental results show that this method has better calibration precision and improves the 3-D measure precision of the system.