Bioceramics have been commonly implemented to replace and restore hard tissues such as teeth and bones in recent years. Among different bioceramics, Baghdadite (BAG) has high bioactivity due to its ability to form apatite and stimulate cell proliferation. So, this structure is used widely for medical applications to treat bone-based diseases. Physically, we expect changes in temperature and pressure to affect the Baghdadite-based nanostructure’s mechanical behaviour. So, in this computational study, we report the pressure/temperature effect on Baghdadite matrix with nanoscale size by using Molecular Dynamics (MD) approach. To this end, physical values like the total energy, temperature, final strength (FS), stress–strain curve, potential energy, and Young’s modulus (YM) are reported. Simulation results indicated the mechanical properties of Baghdadite (BAG) nanostructure weakened by temperature and pressure increase. Numerically, the FS and YM of the defined structure reach 131.40 MPa/159.43 MPa, and 115.15 MPa/139.72 MPa with temperature/pressure increasing. Therefore, the increase in initial pressure and temperature leads to a decrease in the mechanical properties of nanostructures. These results indicate the importance of the initial condition in the Baghdadite-based nanostructures’ mechanical behaviour that must be considered in clinical applications.