Chemical shrinkage is one of the main reasons leading to the early age deformation of concrete. Hence, the prediction of chemical shrinkage is an important issue for evaluating the deformation of concrete and its influence on the durability of concrete structures. There is still room to improve the accuracy for predicting the chemical shrinkage of cement, because some empirical assumptions were involved in traditional methods such as Paulini equation. In this study a discrete algorithm was proposed to deal with the stoichiometry’s conversion of tricalcium aluminate (C3A) and (tetracalcium aluminoferrite) C4AF with ongoing hydration of cement. Based on this discrete algorithm, the volume evolution of phases in cement paste and the chemical shrinkage of cement were calculated. The chemical shrinkage of cement in W/C 0.3 and W/C 0.4 were simulated using this method and compared with the results of experiments and Paulini equation. It was found that the calculated chemical shrinkage of cement in W/C 0.3 and 0.4 are in good agreement with experiments, respectively. In comparison with Paulini equation, the proposed method was more accurate for predicting the chemical shrinkage of Portland cement, because the nonlinear relationship between the chemical shrinkage and degree of hydration of cement can be simulated by dealing with the stoichiometry’s conversion of C3A and C4AF with ongoing hydration.