Homoepitaxial growth of step-flow single crystal diamond was performed by microwave plasma chemical vapor deposition system on high-pressure high-temperature diamond substrate. A coarse surface morphology with isolated particles was firstly deposited on diamond substrate as an interlayer under hillock growth model. Then, the growth model was changed to step-flow growth model for growing step-flow single crystal diamond layer on this hillock interlayer. Furthermore, the surface morphology evolution, cross-section and surface microstructure, and crystal quality of grown diamond were evaluated by scanning electron microscopy, high-resolution transmission electron microcopy, and Raman and photoluminescence spectroscopy. It was found that the surface morphology varied with deposition time under step-flow growth parameters. The cross-section topography exhibited obvious inhomogeneity in crystal structure. Additionally, the diamond growth mechanism from the microscopic point of view was revealed to illustrate the morphological and structural evolution.