In order to meet the needs of rapid acquisition of morphological information in clinical testing and other fields, a fast three-dimensional morphological reconstruction algorithm requiring only two phase images is proposed. The algorithm obtains the structural boundary of the sample on the corresponding incident light orthographic projection plane from two orthogonal phase diagrams. By establishing and solving the correlation between the two groups of orthogonal two-dimensional data, the three-dimensional coordinates and average refractive index of the sample substructure contour are obtained, and then the quantitative distribution of the physical thickness of each substructure is given to realize the three-dimensional structure reconstruction of the sample. The three-dimensional shape reconstruction of samples with different structural characteristics is carried out through simulation and experiments. The experimental results verify the effectiveness and universality of the proposed algorithm.