The mineral carbonation of phosphogypsum (PG) presents considerable potential for simultaneous CO2 sequestration and high-value utilization of PG. Variations in carbon footprints are crucial for enhancing carbonation efficiency and regulating product formation. This study explores the mechanism of direct CO2 mineralization by PG and the evolution of the resulting product. The results demonstrate that 97.14% of the CaSO4·2H2O in PG can be converted to calcite under conditions including a nitrogen–sulfur molar ratio of 3, a liquid–solid ratio of 6, a CO2 flowrate of 0.4 L/min, and a stirring rate of 800 rpm for 60 min. The carbonation rate exhibits significant variation with time, occurring in three distinct stages. Initially, CO2 reacts with ammonia to form (NH4)2CO3, releasing greater heat. This heat inhibits the dissolution of Ca2+ from PG, resulting in a lower carbonation efficiency, as only a limited amount of Ca2+ reacts with CO32– to preferentially form amorphous CaCO3 (ACC). As CO32– formation reaches equilibrium, the endothermic properties of the reaction between CaSO4 and (NH4)2CO3 promote the dissolution of Ca2+ from PG, further accelerating CO2 mineralization and resulting in significant increases in carbonation efficiency and ACC production. The ACC is rapidly transformed into calcite via a “dissolution-reprecipitation” mechanism. However, the carbonation rate of PG decreases as saturation is approached, mainly resulting from the aggregation of fine CaCO3 particles on the PG surface. As a result, the direct CO2 sequestration process by PG follows a carbon footprint sequence of “CO2–(NH4)2CO3–ACC–calcite”. This study provides significant insights into the mechanisms of direct CO2 mineralization and product evolution and offers a basis for optimizing carbonation processes enhancement and regulating product phases.