An embodiment of the invention discloses a multi-tree structure database design method. The multi-tree structure database design method comprises the following steps of establishing a node information table and a node relational table; correspondingly changing the element basic information of a changed element in the node information table when element change is generated; inquiring element rule serial numbers which are corresponding to different trees in the node relational table according to an element serial number of the changed element and other attached condition information of the changed element and generating into new element rule serial numbers based on a father node element serial number of the changed element and the element rule serial numbers; updating the element rule serial numbers of involved change records in the node relational table according to a change type of the changed element. The multi-tree structure database design method can reduce internal storage resource consumption, improve the tree inquiring and processing efficiency and achieve change of multi-tree nodes in real time.