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In this research, we have developed a variable baseline stereo tracking vision system using a 1ms high-speed vision system and a high-speed linear slider. The vision system tracks a moving object, captures a stereo image pair and estimates its distance in only 1ms. It also calculates stereo matching and estimates its 3D shape every 2ms. The high speed linear slider moves stereo cameras horizontally and independently so the baseline length can be changed. We also propose a baseline control method which is adaptive to the distance to the object. When the object appears large in the image, the system reconstructs its 3D shape, and when the object appears small in the image, the system only estimates the 3D position of its center of gravity. The experimental results show that the proposed baseline control method improves the depth accuracy and the system can track and estimate the 3D shapes of fast moving objects.