Provided are a method and apparatus for detecting bio-complexes that are important sub protein interaction networks using a rule-based template in large interaction networks present in a single species. The method includes (a) defining a rule-based template corresponding to a bio-complex to be detected by defining a node that consists of at least one protein, a triplet that consists of two defined nodes and a protein interaction relationship therebetween, and single and composite rules using the triplet and an operator; (b) analyzing the rules of the defined rule-based template by analyzing whether the protein corresponding to the node included in the defined rule-based template and the protein interaction relationship corresponding to the triplet are present in a protein interaction network; and (c) detecting a bio-complex in the protein interaction network by assessing the triplet included in the rules analyzed and the node included in the triplet using a protein interaction relationship and protein of the protein interaction networks.