This work compares the performance of cluster-based and tree-based routing protocols. Two kinds of operations are considered: aggregation and acquisition. We theoretically analyze the performance of cluster-based and tree-based topologies, and find that cluster-based topology is more energy efficient for aggregation than tree-based topology; but in the case of acquisition, tree-based topology is more energy efficient than cluster-based topology. In addition, simulations between HEED and MintRoute routing protocols verify above analysis results. This work can be used to guide the design of application-specific routing protocols selection.