The invention discloses a substance shape measuring device with micro inertial navigation, which comprises a probe group for shape data collecting, a strapdown inertial navigation system and a data storage; the probe group for shape data collecting consists of a row of stretchable probes with pressure sensors, the strapdown inertial navigation system consists of a micro inertia measuring unit and a navigation computer, implements alignment and then measures one surface of a substance, and further implements the alignment and the measurement till the end, and the substance shape is computed by processing software. The substance shape measuring device with micro inertial navigation has free movement, can measure the internal and external shape of the substance with a convenient posture, and has small volume, convenient operation, low cost and easy application generalization. The substance shape measuring device with micro inertial navigation is applicable for the accurate measurement of the size, shape and mutual position of three-dimensional complicated substances in the field of machinery, construction, aviation, spaceflight, war industry, automobiles and commercial manufacture, etc., particularly for the reverse engineering of various substances.