The invention discloses a stereoscopic crossing type warehouse system. The stereoscopic crossing type warehouse system comprises a goods shelf which is provided with a plurality of first goods shelvesand a plurality of second goods shelves in a crossing manner, wherein any one of the first shelves comprises multiple layers of goods placement plates which are arranged mutually in parallel; the plurality of second goods shelves are respectively erected on the second layer of goods placement plate and more than the two layers of goods placement plates from bottom to top; a distance between the two adjacent second goods shelves erected on the same layer of any one of the goods placement plates is more than the width of any one of the second good shelves; a plurality of goods shelf vehicles are arranged on the plurality of second goods shelves in the extension directions of the plurality of second goods shelves; a plurality of driving motors are respectively used for driving the multiple layers of goods shelf vehicles; a controller communicates with the plurality of driving motors; and a remote controller communicates with the controller. According to the stereoscopic crossing type warehouse system disclosed by the invention, based on the plurality of first goods shelves, the plurality of second goods shelves are additionally arranged, and the stereoscopic crossing type warehouse system can make much use of a space in a warehouse in a stereoscopic crossing type, so that the warehousing cost is reduced, and loading or unloading is more convenient.