Weak self-interaction plays an important role in interpreting the biomechanisms and modes of drug action. The structure-dependent self-association of five phenolic acids with various bioactivities, including danshensu (DSS), caffeic acid (CA), rosmarinic acid (RA), lithospermic acid (LA), and salvianolic acid B (SA), was investigated by (1)H NMR. These phenolic acids have similar condensed structures, with a CA moiety and varying numbers of DSS moieties. The strengths of the self-association constants are in the order DSS < CA < RA < LA < SA, which corresponds to the increasing molecular size of these phenolic acids and roughly corresponds to the increasing number of DSS moieties. The binding site for the self-aggregation of these phenolic acids has been identified to be on the CA moiety, rather than on the DSS moiety, as a result of CA's stronger aromatic π-π interactions, which cause larger chemical shift variations. The thermodynamic parameters for the self-association of these phenolic acids show that the self-association is spontaneous and enthalpically favorable at room temperature in all cases. It was inferred that π-π interactions and intermolecular hydrogen bonding stabilize the stacking structures of the phenolic acids. Knowledge of self-association processes will enable us to quantitatively assess the possible effects of self-aggregation on the interaction between drug and protein.