The precise intra-stroke stopping of a pneumatic cylinder is considered extremely dificult because of the time lag due to the compressibility of air and delay of the control valves. Our previous study using a labyrinth-type seal was able to precisely control both the desired intra-stroke stopping and position holding under a time-variant loading condition to a precision of 1 μm. In this study, two types of new control methods, pressure switching and re-positioning, for sub-micron intra-stroke stopping were developed. By using these methods, intra-stroke stopping of a cylinder with a precision of 0.1μm at high-speed moving could be achieved.