The invention provides a three-dimensional warehouse capable of fast transferring middle express items. The three-dimensional warehouse comprises a warehouse unit, a storing and taking device and a control module. The storing and taking device comprises a carrying unit, a transferring unit and an article conveying mechanism. The warehouse unit is a multi-layer storage rack supported by trundles, and packaging boxes store the express items. The carrying unit comprises an outer frame, a drive part and a carrying table. The drive part drives the carrying table to store or take the packaging boxes from the storage rack. The control module generates different item taking sequences according to the express item category or the express item sequences input into the three-dimensional warehouse to control the carrying unit to take goods. The carrying unit takes the express item packaging boxes out of the warehouse unit or the goods collecting position of the three-dimensional warehouse according to the item taking sequences and places the express item packaging boxes on the goods conveying mechanism. When the transferring unit receives the item taking sequences from the article conveying mechanism, a transferring door is closed, and after the item taking sequences are received, the transferring door is opened to enable all express item packaging boxes in the item taking sequences to be sent out through a transfer conveying channel. The three-dimensional warehouse is simple in structure and easy to build, and the warehouse space can be moved and can be extended conveniently.