To investigate the mechanism of local porosity modification in a carbonate reservoir caused by the acidic components associated with natural gas generation, a numerical model for the charging of natural gas rich in acidic components (CO2) was developed. The acidic components are originated from maturation of organic matter in the source rock. The model includes coupled gas-water-rock interactions, multiphase flow, and spatial heterogeneities of the geochemical reactions. The simulation results indicate the following. (1) When regional groundwater travels through the gas- water contact (GWC), it is acidified by the CO2(g) in the gas zone and will dissolve carbonate minerals to form local secondary porosity. The generated local secondary porosity is approximately 0.04 (volume fraction), with a maximum value of approximately 0.27, and is located mainly in the vicinity of the GWC. (2) Under reservoir conditions, the solubility of calcite is much higher than dolomite. The higher solubility and common ion effect of Ca results in calcite being the primary reactive mineral in pure carbonate reservoirs (having both calcite and dolomite). The presence of anhydrite in the system does not change this situation. (3) The groundwater flow field causes GWC evolution to be S-shaped. The inflection and gentle-sloping parts at both ends of the GWC have different angles with the groundwater stream lines, resulting in different amounts of mineral dissolution and precipitation and porosity increase. (4) The limited amount of CO2 from the source rock and groundwater flow in the subsurface seems to be sufficient to support local secondary porosity generation.