The structure of Web site became more complex than before. During the design period of a Web site, the lack of model and method results in improper Web structure, which depend on the designer’s experience. From the point of view of software engineering, every period in the software life must be evaluated before starting the next period’s work. It is very important and essential to search relevant methods for evaluating Web structure before the site is completed. In this work, after studying the related work about the Web structure mining and analyzing the major structure mining methods (Page-rank and Hub/Authority), a method based on the Page-rank for Web structure evaluation in design stage is proposed. A Web structure modeling language WSML is designed, and the implement strategies for evaluating system of the Web site structure are given out. Web structure mining has being used mainly in searth engines before. It is the first time to employ the Web structure mining technology to evaluate a Web structure in the design period of a Web site. It contributes to the formalization of the design documents for Web site and the improving of software engineering for large scale Web site, and the evaluating system is a practical tool for Web site construction.