Precision optical components are extensively used in critical fields such as astronomical observation, space exploration, and projection lithography objectives. These components are characterized by high surface quality, precise profile accuracy, and minimal surface damage. Polishing is the final step in the finishing process of optical elements, requiring an iterative “measurement-processing” cycle to achieve nano-level surface accuracy and sub-nano-level surface roughness. After off-line measurement of the surface shape, the workpiece must be re-installed and aligned on the machine tool twice to ensure precise positioning and posture, which is crucial for subsequent processing accuracy. Traditional contact-based alignment and positioning methods suffer from inefficiencies and risks of surface scratches. To address these issues, this paper proposes a non-contact in-place measurement system for vertical five-axis machine tools, utilizing a spectral confocal sensor. A mathematical model is developed for both the measurement system to obtain workpiece surface coordinates and for the calibration of the spectral confocal sensor on the machine tool. Additionally, a compensation calibration method based on a standard ball is introduced, using a spherical constraint equation. The feasibility and accuracy of this calibration method are validated through practical calibration experiments on a magnetorheological polishing machine tool. Finally, a workpiece position and pose measurement experiment is conducted, with the accuracy of the spectral confocal non-contact in-place measurement system verified against a Renishaw three-coordinate in-place measurement system. Experimental results show that the diameter error of the standard ball is less than 6 μm, and the workpiece positioning error is less than 10 μm, meeting the positioning accuracy requirements for magnetorheological polishing.