Acquiring comprehensive knowledge of protein in various subcellular localizations is one of the fundamental goals in cell biology and proteomics. Although recent large-scale experimental and proteomics studies of S. cerevisiae protein subcellular localizations are archived in various databases, only a few studies use a systems biology approach to characterize S. cerevisiae proteins at a subcellular localization level. Based on the topological properties and biological properties of S. cerevisiae proteins, we have compared, contrasted and analyzed the statistical properties across eight different subcellular localizations. Significant differences are found in all topological properties and biological properties among eight protein categories. Network topology analysis indicates that the nuclear proteins differ from the other seven protein categories, and tend to have the most important topological properties and play an important role in the network, including the highest degree, core number, and betweenness centrality. In the light of the above, we hope these findings presented in this study may provide important help for protein subcellular localization prediction in S. cerevisiae and provide many new insights for understanding the proteins directly from subcellular localizations.