Abstract: Ma-Xing-Shi-Gan Decoction is a classic prescription. However, the interaction among multiple components of the decoction and the change of phase state are not clear. Moreover, the relationship between the physical phase state aggregated by multiple components and the efficacy still needs to be studied. In this study, we monitored the particle size changes of Ma-Xing-Shi-Gan Decoction in real time. Then we isolated different phase states by centrifugation, analyzed their composition distribution and tested their antibacterial activity. We added chemical interference agents to investigate the interaction of multi-component physical phase states accompanied by the observation of particle size change and morphology. We also studied the correlation between antibacterial activity and physical structure of phase states. The results showed during boiling process the degree of hybridization of particles was decreased and the particle size distribution was narrowed and stabilized at 170 nm. The distribution of organic and inorganic components was heterogeneous among different phase states. S-13500, supernatant isolated by 13 500×g centrifugation, constituted by ephedrine, amygdalin, glycyrrhizic acid and inorganic components Ca, K, Mg, etc., had the strongest antibacterial activity. The molecular interaction force in the active physical phase state was mainly hydrophobic and hydrogen bond. The destruction of the interaction force will lead to the change of phase structure and the decrease of antibacterial activity in vitro and in vivo. This study confirms that, in the boiling process of the Ma-Xing-Shi-Gan Decoction, the chemical components interweave and interact to form new physical phase states, leading to heterogeneous distribution of components. The antimicrobial activity of the active phase depends on both chemical composition and physical structure, which provides a direct evidence for the physical basis of the efficacy of traditional Chinese medicine.