For multilayer films system, in order to obtain the thickness and surface profile in each layer of thin film, a method to measure the 3D morphology of a multilayer films system based on scanning white light interferometer has been proposed in this article. At first, the mathematical relationship between reflection phase and thickness of each film layer has been obtained by using the electromagnetic field boundary conditions. Then, a nonlinear least square algorithm has been used to fit the reflection phase which had been found through a scanning white light interferometer, in this way the linear and nonlinear terms of the reflection phase have been separated, which made it possible to measure top-layer surface profile and thickness of each thin film layer respectively and avoided the interference with each other, because the linear term is related to the top layer’s surface profile but the nonlinear term is correlated to the thickness of each film layer in multilayer thin films system. Thus, the three-dimensional morphology of multilayer thin films system could be reconstructed. Experimental results showed this method was effective in the three-dimensional morphology measurement for multilayer thin films. And the measurement could be completed just using the existing commercial scanning white light interferometer, as a consequence the measurement cost is low, and the operation will be quite simple.