An L-proline containing amphiphilic dipeptide was found to self-assemble into nanosphere and nanofiber structures. These nanostructures could catalyze an asymmetric aldol reaction in water. Good reactivity and enantiomeric selectivity was observed for the nanosphere structure. Although the reaction could be catalyzed by the nanofiber structure, its enantioselectivity was remarkably decreased. It was suggested that the appropriate packing of the chiral assemblies can selectively control the access of the reactants and thus lead to a higher enantioselectivity in the chirality matched structures.