Sr-hydroxyapatite has drawn much attention with promising applications in biomedical engineering especially in drug delivery and tissue repair. A novel protocol for the preparation of Strontium hydroxyapatite (Sr-HAP) and Strontium hydroxyapatite encapsulated by graphitic carbon nitride (Sr-HAP@gCN) with high purity and better homogeneity was adopted for potential use in orthopaedic surgeries. The physiological pathway of Strontium and calcium inside humans follow the same trend leading to the mineral deposition of the bone. In the present study, a novel attempt in synthesizing Sr-HAP and Sr-HAP@gCN by the hydrothermal method is proposed for obtaining an ideal biomaterial with potential biocompatibility and pharmacological activity. Phase identification by X-ray diffraction (XRD), Fourier transform Infra-Red spectroscopic analysis (FTIR), Electron & atomic force microscopic studies, Thermogravimetric and Raman spectroscopic analysis was performed on the prepared Sr-HAP and Sr-HAP@gCN to characterize the incorporation efficiency of Strontium. Resazurin microtiter assay and MTT assay were used to evaluate antimicrobial susceptibility and biocompatibility. The typical crystal phase of Sr-HAP and a phase change in Sr-HAP@gCN have been demonstrated with special reference to the interfacial connection between gCN and Sr-HAP through FT-IR studies. Raman spectroscopy revealed the archetypal signature of symmetric and asymmetric PO vibrations pertaining to linearity change with the addition of Strontium. The biological effect of Sr-HAP and Sr-HAP@gCN was quite significant in inducing mineralization when kept immersed in simulated body fluid (SBF) for 21 days. Promising results pertaining to antimicrobial susceptibility and biocompatibility have been proved as an encouraging choice for drug delivery applications and bone filling applications.