There are many cases that many XML documents have different DTDs in spite of having a similar structure and being logically same kind of document. For this reason, It occurs a problem that these XML documents have different database schema and are stored in different databases. So, in this paper, we propose an algorithm that unifies DTDs of these XML documents using the finite automata and the tree structure. The finite automata is suitable for representing repetition operators and connectors of DTD, and is a simple representation method for DTD. By using the finite automata, we are able to reduce the complexity of algorithm. And we apply a proposed algorithm to unify DTDs of science journals.