In order to make the process of generating small traffic zones into middle traffic zones more reasonable and taking the similarity and the positional relation of small traffic zones into consideration, two-dimensional graphic theory-clustering method on the mergence of small traffic zone is applied. Given conditions that satisfied the adjacent small traffic zones, the positional relation of small traffic zones by the adjacent matrix is re-formulated. After the undirected weighted graph construction, the minimum spanning tree (MST) was solved. Choose the threshold according to the MST for the small traffic zones mergence. Finally the F-test is used to determine the optimal mergence in theory which is the reference of the selection of the small traffic zone mergence. The result of example analysis shows that the clustering number reduces along with the increase of the threshold value, and only the similar and adjacent small traffic zones can be merged during the mergence. In addition, the F-test is adopted to determine the exclusive optimal scheme of mergence for reference, which proved that the division result was feasible.