In this study, an XYθ position sensor is designed/proposed to realize the precise control of the XYθ position of a holonomic inchworm robot in the centimeter to submicrometer range using four optical encoders. The sensor was designed to be sufficiently compact for mounting on a centimeter-sized robot for closed-loop control. To simultaneously measure the XYθ displacements, we designed an integrated two-degrees-of-freedom scale for the four encoders. We also derived a calibration equation to decrease the crosstalk errors among the XYθ axes. To investigate the feasibility of this approach, we placed the scale as a measurement target for a holonomic robot. We demonstrated closed-loop sequence control of a star-shaped trajectory for multiple-step motion in the centimeter to micrometer range. We also demonstrated simultaneous three-axis proportional–integral–derivative control for one-step motion in the micrometer to sub-micrometer range. The close-up trajectories were examined to determine the detailed behavior with sub-micrometer and sub-millidegree resolutions in the MHz measurement cycle. This study is an important step toward wide-range flexible control of precise holonomic robots for various applications in which multiple tools work precisely within the limited space of instruments and microscopes.