Abstract: The confocal laser scanning microscopy (CLSM) system is a high-precision instrument for three-dimensional (3D) topography measurement of micro-nano structured surfaces. This study systematically optimized traditional confocal technology through two key advancements. First, to address edge overshooting in scanning images, an innovative scanning trajectory and waveform design was developed, achieving linear scanning control in the galvanometer-based scanning system. This significantly improved scanning stability and signal-to-noise ratio(SNR). Second, the integration of a relay amplification optical system effectively enlarged the spot size in the detection focal plane, substantially reducing the operational complexity of pinhole alignment and enhancing the system’s practicality. Finally, experimental validation demonstrates that under the optical path conditions of 488 nm laser light source, 0.4 numerical aperture and 50 μm pinhole, the optimized system could demonstrat excellent performance. Its lateral resolution reaches 400 nm, and the axial resolution is better than 30 nm, providing a more accurate solution for three dimensional topography measurement at the micro-nano scales.