The present application provides a method, apparatus and system for controlling transportation between warehouses. The method includes: receiving, from the source RCS, first transportation information which includes information of a first to-be-transported object; transporting the first to-be-transported object to a handover area; transferring control over the AGV from the source RCS to the target RCS; receiving a location of a first target storage space from the target RCS; transporting the first to-be-transported object from the handover area to the first target storage space. In the present application, the AGV transfers the control over itself from the source RCS to the target RCS after moving the to-be-transported object to the handover area, such that the target RCS could take over the AGV and control the AGV to transport the first to-be-transported object from the handover area to the first target storage space. In this way, a fully automatic transportation is achieved, improving the efficiency of transporting and warehousing compared to manual transporting.