In indexing and organizing Web resources, there have been two basic methods: automatic indexing by extracting key words and library classification schemes or subject directories of search engines. But, both methods have failed to satisfy the user's information needs, due to the lack of standard criteria and the irrationality of its structural system. In this paper I have examined the limits of library classification scheme's structures and the problems related to the nature of Web resources such as specificity and exhaustivity. I have also attempted to explain the logicality of Web resources organization by facet analysis and its strengths and limitations. In so doing, I have proposed three specific methods in using facet analysis: firstly, indexing system by facet analysis; secondly, the alternative transformation of the enumerative classification scheme into facet classification scheme; and finally, the facet model of subject directory of domestic search engine. After examining the three methods, my study concludes that a controlled vocabulary by facet analysis can be employed as a useful method in organizing Web resources.