Having excellent biocompatibility and apatite mineralization as well as efficient mechanical properties makes bredigite as one of the most attractive bioceramics. A beam-type porous biological implant in a 3D-printed architecture is designed with micron pore size. The surface properties, morphology, and size of the composed powders are evaluated using Scherrer and Williamson-Hall equation. The effect of MNPs deposition into the bredigite bioceramics and correlation with temperature effect on roughness of the prepared bio-nanocomposite are also investigated for hyperthermia application potential. The composed powders are characterized by x-ray diffraction, and then scanning electron microscopy (SEM), differential scanning calorimetry, thermogravimetric analysis (weight change, TGA), and atomic force microscopy are utilized to evaluate the surface topography. The resonance response is the tendency of a bone scaffold to respond at prominent amplitude while the frequency of its oscillations is equal to the structure’s natural frequency of vibration. Therefore, based on the obtained mechanical properties via the experimental approach for the bio-nanocomposite material, an analytical solution based upon the multiple-timescale method is carried out to analyze the nonlinear primary resonance of a 3D-printed porous beam-type biological implant under uniform-distributed load. According to SEM observations, there are hard agglomerates in the bredigite-magnetite nanoparticles (Br-MNPs) bio-nanocomposite material with low weight fraction of MNPs. However, they are broken down by increasing the amount of MNPs. Also, it is displayed that for lower MNPs weight fraction, the height of jump phenomenon related to the nonlinear resonance response is maximum and minimum for, respectively, irregular and mesoporous shapes of morphology, but their associated forcing amplitudes related to the bifurcation points are minimum and maximum, respectively.