As flexible joint is a typical low-rigidity micro part, which have four narrow neck structures evenly distributed around its central axis, it is necessary to strictly control the dimensional accuracy of the narrow necks to improve the consistency of stiffness. However, the radius of the arc of the narrow necks is less than 2mm, and the thickness of thinnest part of the necks formed by two adjacent arcs is only tens of microns, which also has sub-micron accuracy requirement. These cross-scale dimensional characteristics and accuracy requirements give rise to extremely difficulty on the measuring process. In this paper, an on-machine measurement method for the semicircular narrow necks was presented and a measuring device was developed based on the comparative principle by making full use of the high linearity characteristic in the small measuring range of the sensor probes. Meanwhile, the on-machine measurement process based on ultra-precision machine tools was also introduced in details. The experiments results show that the uncertainty of the measurement method proposed is less than 0.2µm, and the repeatability is less than 0.1μm, which meet the measuring requirement of flexible joint. Furthermore, the effect of probe position, measurement force, environmental factor and the accuracy of the sensor on total measuring accuracy was analyzed, which could provide further evidences to improve the measuring accuracy. of micro-scale hybrid surface texture.