The study aims to improve Web navigation efficiency by reorganizing Web structure. Navigation efficiency is defined mathematically for both navigation with / without target destination pages, e.g. for experienced and new users. To help experienced users not to lose their orientation, structure stability is taken into consideration. Stability constraint can also help website designers control the maintaining effort of Web. This study proposes a mathematical programming method to reorganize Web structure in order to achieve better navigation efficiency. Designer can specify the user requirements and how stable the website structure should be. An e-banking example is given to illustrate how the method works in scenarios where user surfs with target destination. This study has the advantage of assessing and improving navigation efficiency and of relieving the designer of tedious chore to modify the structure in transformation.