In this paper, the flexible and efficient warehouse with combination of Rail Guided Vehicle (RGV) and lift was the research object. In order to solve the problem that the traditional high speed stacker spatial warehouse cannot meet the high beat capacity Jobs Per Hour (JPH) of 60 Units/h, this spatial warehouse adopted RGV conveying in the horizontal plane and lift conveying in the vertical direction. CAD software was utilized to plan and design the two-dimensional plan of the spatial warehouse, Catia software was adepted to design the three-dimensional model of the corresponding three-dimensional warehouse, and Plant Simulation software was used to verify whether the solution can meet the high beat capacity, and the economic investment was compared with that of the traditional stacker three-dimensional warehouse through cost calculation. The final conclusion is that this flexible and efficient three-dimensional warehouse can meet the JPH 60 Units/h beat capacity and the economic cost is lower than the traditional three-dimensional warehouse, which has wide application prospect.