The absence of a conducive bone formation microenvironment between fractured ends poses a significant challenge in repairing large bone defects. A promising solution is to construct a bone formation microenvironment that mimics natural bone tissue. Biomimetic mineralized collagen possesses a chemical composition and microstructure highly similar to the natural bone matrix, making it an ideal biomimetic bone substitute material. The microstructure of biomimetic mineralized collagen is influenced by various factors, and its biomineralization and microstructure, in turn, affect its physicochemical properties and biological activity. We aimed to utilize mineralization time and solution concentration as variables and employed the polymer-induced liquid precursor strategy to fabricate mineralized collagen with diverse microstructures, to shed light on how mineralization parameters impact the material microstructure and physicochemical properties. We also investigated the influence of microstructure and physicochemical properties on cell biocompatibility and the bone-forming microenvironment. Through comprehensive characterization, we examined the physical and chemical properties of I-EMC under various mineralization conditions and assessed the in vitro and in vivo biocompatibility and osteogenic performance. By investigating the relationship between mineralization parameters, material physicochemical properties, and osteogenic performance, we revealed how microstructures influence cellular behaviors like biocompatibility and osteogenic microenvironment. Encouragingly, mineralization solutions with varying concentrations, stabilized by polyacrylic acid, successfully produced intrafibrillar and extrafibrillar mineralized collagen. Compared to non-mineralized collagen, all mineralized samples demonstrated improved bone-forming performance. Notably, samples prepared with a 1× mineralization solution exhibited relatively smooth surfaces with even mineralization. Extending the mineralization time enhanced the degree of mineralization and osteogenic performance. Conversely, samples prepared with a 2× mineralization solution had rough surfaces with large calcium phosphate particles, indicating non-uniform mineralization. Overall, our research advances the potential for commercial production of mineralized collagen protein products, characterized by dual biomimetic properties, and their application in treating various types of bone defects.