Many clustering algorithms are unable to solve the clustering problem of protein-protein interaction (PPI) networks effectively. A novel clustering model which combines the optimization mechanism of artificial bee colony (ABC) with the fuzzy membership matrix is proposed in this paper. The proposed ABC-IFC clustering model contains two parts: searching for the optimum cluster centers using ABC mechanism and forming clusters using intuitionistic fuzzy clustering (IFC) method. Firstly, the cluster centers are set randomly and the initial clustering results are obtained by using fuzzy membership matrix. Then the cluster centers are updated through different functions of bees in ABC algorithm; then the clustering result is obtained through IFC method based on the new optimized cluster center. To illustrate its performance, the ABC-IFC method is compared with the traditional fuzzy C-means clustering and IFC method. The experimental results on MIPS dataset show that the proposed ABC-IFC method not only gets improved in terms of several commonly used evaluation criteria such asprecision,recall, andPvalue, but also obtains a better clustering result.