XML document data encoding scheme is foundation of XML document query processing. A good document encoding mode can improve the efficiency of XML document query. In order to resolve the inefficiency for XML data query and support dynamic updates, etc, this paper has proposed an improved method to encode XML document nodes. On the basis of the binary traversal, it introduces the trigeminal linked list storage structure of binary tree for encoding. It takes natural number as the serial number of the node encoding, so the encoding length is shorter. Besides, node parent pointer is used for encoding, which will facilitate to determinate the relationship between element nodes. Due to trigeminal linked list storage of nodes, the operation of the document update is more convenient.