The invention relates to the technical field of biomedical materials, and particularly relates to a BMP microsphere loaded 3D printing porous metal stent and a preparation method thereof. According to the invention, a loaded microsphere-containing three-dimensional micro-stent is built in each hole of a 3D printing titanium stent. The problem that in the prior art, because the diameter of a hole is overlarge, cells only can be subjected to climbed growth on the two-dimensional space of the wall of the hole, and difficult to be subjected to three-dimensional hierarchical growth in the whole hole is solved, and by filling the three-dimensional micro-stent with a rhBMP-2 or rhBMP-7 loaded chitosan microsphere, a better growth and differentiation environment is provided for cells, thereby further promoting the combination of bone tissues and the stent. The three-dimensional micro-stent provided by the invention makes the complete healing of numerous patients with bone tissue defect caused by illnesses and accidents and the like possible; the three-dimensional micro-stent can also be used as a novel interbody fusion instrument, and applicable to an interbody fusion surgery, therefore, the three-dimensional micro-stent has an important clinical application value.