The periodontal structure is a particularly exquisite model of hierarchical spatial control of mineralization. Extracellular matrix control in the selective mineralization of the periodontium complex remains elusive since the extracellular matrix is a set of mineralization promoters and inhibitors. The phosphorylated proteins, which are ubiquitous in the extracellular matrix of the periodontium complex, are well-documented as primary factors in the regulation of tissue mineralization. Whether organic phosphates are key regulators in defining the interfaces between dentin, cementum, periodontal ligament and alveolar bone is an issue worthy of research. Here, we investigated the in vitro remineralization process of demineralized and dephosphorylated periodontal tissue sections. When exposed to a metastable mineralization solution, a large number of calcospherulites deposited on the surface of the dephosphorylated sections and the tissue selective mineralization were disrupted. Interestingly, on adding a dentin matrix protein-1 analogue named polyacrylic acid, the surface mineralization rate in the dephosphorylated periodontal complex reduced dramatically. In contrast, hierarchical mineralization was displayed by the demineralized section at the tissue collagen fibrillar levels in both alveolar bone and dentin regions. These results demonstrated that the organic phosphate could prevent surface mineral deposition, and the minerals could penetrate the collagen fibrils to initiate a selective and hierarchal tissue mineralization with the assistance of the dentin matrix protein-1 analogue in the periodontal complex. This study enhances our understanding of the mineralization discrepancy in the periodontal tissues, which will provide some insight into the development of biomaterials for the regeneration of soft-hard tissue interfaces.