A multi-segment rotary shaft structure includes a driving joint assembly and a driven joint assembly. The driving joint assembly at least includes two opposite joint plates and a middle link plate assembly engaged therebetween. The driven joint assembly is disposed between the opposite joint plates and includes at least two driven plates. Opposite ends of the driven plates are formed with synchronous driving sections drivingly engaged with each other. Inward ends of the opposite joint plates are linked with outward ends of the driven plates. Outward ends of the middle link plate assembly are linked with the inward ends of the driven plates. The driving joint assembly and driven joint assembly are stringed and pivotally connected and combined, whereby the joint plates can be freely rotated around multiple rotational centers.