Naturally occurring carbonates have a wide variation in Mg and Ca contents. Using the density-functional-theory calculations, this study examines the effect of Mg and Ca concentrations on bond lengths and equilibrium fractionation factors of Mg-Ca isotopes among calcite-type carbonate minerals (MgxCa1−xCO3). Mg content x and Ca content (1−x) of the investigated carbonate minerals range from 1/12 to 1 and from 1/36 to 1, respectively. Concentration of Ca and Mg in carbonates have significant effects on Ca–O and Mg–O bond lengths when x is close to 0, 0.5 or 1. Because equilibrium isotope fractionation factors (103lnα) are mainly controlled by their relevant bond strengths, which can be measured using their average bond lengths, 103lnα of 26Mg/24Mg and 44Ca/40Ca between calcite-type carbonate minerals and dolomite also vary dramatically with Mg content, especially when x is close to 0 and 1. For instance, at 300 K, 103lnα of 26Mg/24Mg between Mg1/12Ca11/12CO3 and dolomite (x = 0.5) is ∼−4.3‰, while 103lnα of 44Ca/40Ca between Mg23/24Ca1/24CO3 and dolomite is ∼6‰. Dolomite is enriched in 26Mg but depleted in 44Ca relative to all other carbonate minerals, which is consistent with it having the shortest Mg–O bond length and the longest Ca–O bond lengths among all carbonates. At 300 K, a small change of x from 0.5 to 0.6 in dolomite could result in 1‰ variation in 103lnβ of 26Mg/24Mg. Therefore, the concentration effect in carbonate minerals should be taken into account when applying the isotope fractionation factors of carbonate minerals to understand geochemical processes.