In the modern rapid growing web era, the scope of web publication is about accessing the web resources. Due to the increased size of web, the search engines face many challenges, in indexing the web pages as well as producing result to the user query. Methodologies discussed in literatures towards clustering web documents suffer in producing higher clustering accuracy. Problem is mitigated using, the proposed scheme, Semantic Conceptual Relational Similarity (SCRS) based clustering algorithm which, considers the relationship of any document in two ways, to measure the similarity. One is with the number of semantic relations of any document class covered by the input document and the second is the number of conceptual relation the input document covers towards any document class. With a given data set Ds, the method estimates the SCRS measure for each document Di towards available class of documents. As a result, a class with maximum SCRS is identified and the document is indexed on the selected class. The SCRS measure is measured according to the semantic relevancy of input document towards each document of any class. Similarly, the input query has been measured for Query Relational Semantic Score (QRSS) towards each class of documents. Based on the value of QRSS measure, the document class is identified, retrieved and ranked based on the QRSS measure to produce final population. In both the way, the semantic measures are estimated based on the concepts available in semantic ontology. The proposed method had risen efficient result in indexing as well as search efficiency also has been improved.