Relevant uncertainties of theoretical atomic data are vital to determining the accuracy of plasma diagnostics in a number of areas, including, in particular, the astrophysical study. We present a new calculation of the uncertainties on the present theoretical ion-impact charge exchange atomic data and X-ray spectra, based on a set of comparisons with the existing laboratory data obtained in historical merged-beam, cold-target recoil-ion momentum spectroscopy, and electron beam ion traps experiments. The average systematic uncertainties are found to be 35–88% on the total cross sections, and 57–75% on the characteristic line ratios. The model deviation increases as the collision energy decreases. The errors on total cross sections further induce a significant uncertainty to the calculation of ionization balance for low-temperature collisional plasmas. Substantial improvements of the atomic database and dedicated laboratory measurements are needed to obtain the current models, ready for the X-ray spectra from the next X-ray spectroscopic mission.