To assess the velocity stability of CO spectral lines in the Milky Way Imaging Scroll Painting (MWISP) survey, we employ a cross-correlation method to measure velocity shifts across ∼10,000 CO spectra from six reference sources observed over the ten-year duration of the survey. The standard deviations (σ) of these measured velocity shifts range from 0.03 to 0.23 km s−1 for their 12CO lines and 0.03 to 0.16 km s−1 for 13CO lines. We find that larger shifts are associated with broader linewidths, more pronounced differences between monthly and long-term variations, and a stronger correlation between velocity shifts of 12CO and 13CO lines. By examining the relation of velocity shifts with the Azimuth–Elevation of the telescope, as well as the velocity fields of these extended sources, we find that the velocity shifts exhibit systematic changes across different Azimuth–Elevation ranges. The patterns and amplitudes of these changes vary among sources and are closely linked to the extended velocity fields of sources. This indicates that the increased velocity shifts are primarily caused by pointing errors, which are more sensitive to reference sources with higher velocity gradients. We also provide high signal-to-noise, velocity-aligned template spectra for reference sources.