Dolomitization is controlled by numerous interacting factors, causing the mechanism of dolomite reservoir formation to remain unclear. In particular, the influences of lithological minerals and crystal lattice characteristics on dolomitization may be the main driver of large-scale dolomite development. In this study, physical laboratory experiments involving the dissolution, precipitation, and transformation of carbonate minerals were conducted, along with real-time testing and analysis of rock samples and water samples, to determine the mechanism underlying metasomatic dolomitization. Additionally, multiple two-dimensional and three-dimensional homogeneous and heterogeneous numerical models were established. Changes in mineral content, ion concentration, and porosity were calculated using multiphase flow numerical simulation technology, and dolomitization was comparatively analyzed under various lithological conditions. The combination of physical experiments and numerical simulation effectively demonstrated the influence of dolomite crystal nucleus and lattice defects on dolomite formation. The presence of a dolomite crystal nucleus can promote the dissolution of calcite and allow more Mg to enter the calcite crystal lattice, promoting further dolomitization. Dolomitization occurs preferentially at lattice defects, and calcite grain boundaries break easily. The results of this study verify that surface conditions with low temperature and pressure are unsuitable for the development of dolomite, but microbes may produce small dolomite nuclei, leading to the large-scale development of dolomite. In the deep layer, because of defects in the crystal lattice, numerous pores form through dissolution. Because the lattice of deep dolomite is less stable than the lattice of limestone, dolomite has better physical properties than limestone after dissolution.