Understanding the doping behavior of impurity ions in clinker phases is crucial for controlling the doping effect on clinker compounds, which, however, has not yet been fully demonstrated due to the composition complexity. Herein, we employ the state-of-the-art ab initio calculation to uncover the substitution mechanism of Cu ions in 4 dominant clinker crystals. The defect formation energies indicate Cu ions energetically prefer to substitute Fe ions in ferrite, which is in accord with the experiments. The bond order difference is innovatively postulated to interpret the energy barriers of Cu substitution in comparison with the ionic radius criterion. The high potential barriers of Cu substituting Ca, Si, and Al ions are ascribed to their bond order mismatch, while the tendency of Cu replacing Fe is due to their bond order similarity. Namely, the Cu doping in clinker phases follows the bond order conformity principle. In-depth electronic structure analysis reveals that the bond order is more effective than the ionic radius to estimate potential barriers of Cu substitution in complex clinker system mainly because the latter underestimates the influence of electronic structure differences while the bond order directly measures the bonding structure related to interatomic charge transfer.