Compared with other sensing mechanism such as piezoresistive, inductive, etc., capacitive sensing has advantage of high sensitivity, low dynamic mass, high inherent frequency, besides, gap-variable capacitive sensor has flexibility that sensitivity can be improved by sacrificing measurement range. In this paper, a tactile probing system based on capacitive sensor is proposed, the capacitive sensor is innovatively designed to differential capacitor to realize 3D measurement, besides, the capacitive sensor is fabricated by low cost MEMS technique, which ensures the manufacture precision. The project of capacitive sensing based on MEMS technique is originally adopted in this field. Experimental results indicate this probing system be used for submicron measurement of small structures with dimension larger than 0.3 mm and depth down to 2.3 mm.