In the present contribution, the mathematical modeling and numerical solution of the carbonation phenomenon have been investigated for the porous cement mortars. To achieve this goal, the Papadakis analytical proposal has been fully investigated. The molar concentration variations of the hydrate (CSH and Ca(OH)2 ) and unhydrated products (C2S and C3S) have been analyzed during the carbonation. The numerical simulations have been firstly achieved on the 3D numerical mortar samples including the aggregates using the relevant granulometry, whose applications sustain more realistic outcomes. The solution has been done using the FEM for the non-linear transient system of PDEs. The numerical results have been compared to those done from the experiments using the pH detector and Differential Thermal Analysis (DTA). Some conclusions and outlooks pertaining to the carbonation modeling have been emphasized.