Magnesium ions are highly enriched in early stage of biological mineralization of hard tissues. Paradoxically, hydroxyapatite (HAp) crystallization is inhibited significantly by high concentration of magnesium ions. The mechanism to regulate magnesium‐doped biomimetic mineralization of collagen fibrils has never been fully elucidated. Herein, we revealed that citrate could bio‐inspire the magnesium‐stabilized mineral precursors to generate magnesium‐doped biomimetic mineralization as follows: Citrate could enhance the electronegativity of collagen fibrils by its absorption to fibrils via hydrogen bonds. Afterward, electronegative collagen fibrils could attract highly‐concentrated electropositive polyaspartic acid‐Ca&Mg (PAsp‐Ca&Mg) complexes followed by phosphate solution via strong electrostatic attraction. In the meanwhile, citrate adsorbed in/on fibrils could eliminate mineralization inhibitory effects of magnesium ions by breaking hydration layer surrounding magnesium ions and thus reduce dehydration energy barrier for rapid fulfillment of biomimetic mineralization. The remineralized demineralized dentin with magnesium‐doped HAp possessed antibacterial ability and the mineralization mediums possessed excellent biocompatibility via cytotoxicity and oral mucosa irritation tests. This strategy should shed light on cationic ions‐doped biomimetic mineralization with antibacterial ability via modifying collagen fibrils and eliminating mineralization inhibitory effects of some cationic ions, as well as could excite attention to the neglected multiple regulations of small biomolecules, such as citrate, during biomineralization process.This article is protected by copyright. All rights reserved