The controlled synthesis of nanohybrids with magnetic metal oxides (Fe3O4), noble metals Au, and hydroxyapatite (HAp, hydroxyapatite) have received considerable attention for applications in photocatalysis, molecular imaging, drug delivery. Green and multifunctional Fe3O4/HAp/Au composite nanoparticles (NPs) with biocompatibility and magnetism for photocatalyst was developed by a facile method. The overall architecture of nanocomposites is one of the most important factors dictating the physical and chemical properties of nanohybrids with significant advances and various functions. The improvement performance of the Fe3O4/HAp/Au in photocatalysis was evaluated by degradation of organic pollutant (methylene blue, MB) under visible light irradiation. The results showed that the hybrid Fe3O4/HAp/Au NP displayed high photocatalytic activity due to surface plasmon resonance (SPR) of Au, the combination of magnetic NPs and HAps with adsorption, also the mechanism was discussed in detail. The efficient magnetic composite nanoparticles can be separated with target and recover, as well as recycle processes. It proposed novel NPs and methodology to design and fabrication of multifunctional NPs with high quality for application of photocatalysis. Furthermore, it is expected that the safe, green and multifunctional composite NPs will provide an interesting platform not only for photocatalysis, but also for developing molecular imaging probe and drug delivery with target, as well as Raman detection.