Constructing supramolecular materials with tunable properties and functions is a great challenge due to the complex competition between multiple assembly pathways. Herein, we report that dipeptides can self-assemble into aerogels with entirely different surface wettability through precisely controlling the assembly pathways. Charged groups or aromatic residues are selectively exposed on the surface of their nanoscale building blocks which results either in a superhydrophilic or highly hydrophobic surface. With this special property, single component dipeptide aerogels can play diverse roles in medical care applications. This study suggests great promise in the synthesis of supramolecular materials with different targeted functions from the same molecular unit.