The morphology of microstructure in glass micromachining is measured with high precision by digital holographic microscopy. The digital hologram of microstructure is recorded based on the Mach-Zehnder off-axis micro-interference system. The high-precision phase distribution is extracted by hybrid reconstruction algorithm and row-column scanning unwrapping. Then the morphology of microstructure is constructed and the depth is calculated. The morphology of flat， convex spherical microlen is simulated and measured， which verifies feasibility of the method. The surface of the glass slide is micro-machined with a carbon dioxide laser， the effects of different lithography parameters on the morphology and depth of glass microstructure is quantitatively analyzed. And the influence of the recondensed height caused by the processing heat affected zone on the processing quality is analyzed. The results show that the lithography depth increases with the increase of laser power and increases with the decrease of marking speed， and the depth is larger when the Q frequency is smaller. This helps guide the fine processing of the glass.