The homo-dimer, homo-trimer, homo-tetramer, homo-hexamer of proteins were classified with a new encoding method—encoding on the basis of grouped weight (EBGW) and component-couple algorithm. It was found that the overall classification accuracy by Jackknife test was 70.92%, which was 20.28 and 7.53 percentile higher than that of the amino acid composition and that of the weight pseudo-amino acid composition method with the same classifying algorithm on the same data set. The results indicate that EBGW method has reached a satisfying performance despite its simplicity.