This paper proposes a three-dimensional measurement method for small parts with large height and complex reflection characteristics based on microscopic fringe projection measurement technology. A composite microscopic system characterization model based on the traditional camera imaging model and the polynomial fitting model is proposed for the calibration of the measurement system, which is used to solve the complex problem of the microscopic imaging optical path and improve the measurement accuracy of the system. An adaptive multiple exposure measurement method is proposed. And the method solves the problems of overexposure and darkness caused by the optical properties of the micro-structure and the environment. The small depth of field limitation problem of traditional micro measurement technology is solved by the micro-imaging technology of super depth of field. Experiments with a prototype demonstrate the validation and accuracy of the proposed algorithm and system configuration. The root mean square of the reconstruction errors is less than $$0.2\,\mu \hbox {m}$$ with a field of view of 2.4 mm $$\times $$ 3.2 mm and a measurement height of 600 $$\mu $$ m.