Micro-nano measurement represents a critical engineering focus in the advancement of micro-nano fabrication technologies. Exploring advanced micro-nano measurement methods is a key direction for driving progress in micro-nano manufacturing. This study proposes a confocal measurement method utilizing a liquid crystal spatial light modulator (LC-SLM) to simulate a binary Fresnel lens for 3D focusing, enabling the non-mechanical measurement of spatial positions on sample surfaces. Specifically, it introduces a 3D focusing method based on LC-SLM, constructs a confocal microscopy 3D focusing system, and conducts lateral focusing experiments and axial focusing experiments. Experimental results demonstrate that the system can freely adjust lateral focusing positions. Within an axial focusing range of 900 μm, it achieves axial measurement accuracy exceeding 1 μm, with a maximum resolution capability of approximately 16.667 nm. Compared to similar confocal microscopy systems, this method allows rapid adjustment of lateral focusing positions without regenerating phase grayscale maps, achieves comparable axial measurement accuracy, and enhances measurement speed.