Three-dimensional profile measurement is perceived as an indispensable process for deterministic fabrication of aspheric mirrors. In this work, we develop on-machine 3D profile measurement on a subaperture polishing machine, namely, JR-1800. The influences of mechanical errors, misalignments, output stability, temperature variation, and natural vibration are investigated in detail by calibration, mechanical alignment, and finite-element analysis. Two quantitative methods are presented for aligning the turntable, length gauge, and workpiece into together. An error compensation model is also developed for further eliminating misalignments. For feasibility validation, two prototypical workpieces are measured by JR-1800 and an interferometer. The results indicate that JR-1800 has an RMS repeatability of ~λ/30 (λ=632.8 nm). The data provided by the two systems are highly coincident. Direct subtractions of the results from the two systems indicate that the RMS deviations for both segments are less than 0.07 μm.