Relevant uncertainties on theoretical atomic data are vital to determine 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 get the current models ready for the X-ray spectra from the next X-ray spectroscopic mission.