The invention relates to a multi-layer three-dimensional automatic moving seedbed system. The system comprises a cultivation unit (A) and a moving unit (B). The cultivation unit (A) comprises single seedbeds (C) and driving devices (D). The moving unit (B) comprises a lifting table device (E), a chain wheel mechanism (F) and a wheel train mechanism (G), the moving unit (B) is driven by the wheel train mechanism (G) to move, the lifting table device (E) is driven by the chain wheel mechanism (F) to conduct lifting motion and stops at a designated position under the effect of a sensing positioning device, and the lifting table device (E) is provided with a first-stage pushing assembly and a second-stage pushing assembly and can transfer and carry the single seedbeds (C) to the designated position. By means of the system, optimal management of large-scale greenhouse production is achieved; when applied to fast spatial delivery and layout of seedbeds, the system solves the logistics problem in large-scale greenhouse production management, relieves the labor intensity of management staff, increases the utilization rate of greenhouse space per unit area and reduces the seedling culture cost.