In this paper, we have focused that the number of word in the web document affects definite clustering performance. Our experimental results have clearly shown the relationship between the amounts of word and its impact on clustering performance. We also have presented an algorithm that can be supplemented of the contrast portion through co-links frequency of web documents. Testing bench of this research is 1,449 web documents included on 'Natural science' category among the Naver Directory. We have clustered these objects by term-based clustering, link-based clustering, and hybrid clustering method, and compared the output results with originally allocated category of Naver directory.