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Alisols are the main pharmaceutical components of Alisma,a well known herb in Traditional Chinese Medicine (TCM).This paper investigated the molecular interaction mechanism of Alisols and Hemoglobin (Hb) by using Fluorescence and Circular Dichroism spectra in combination with molecular modeling under the simulated physiological conditions.Molecular modeling results that were in agreement with the experimental results revealed that the binding of Alisol B 23-acetate and Hb was much more than that with Alisol A 24-acetate,indicating that the difference was related to the structure of the side chain of which the opened one leads to the strong binding while the folded to the weak so that the former may be the steering group of Alisols.The conclusion should be of great assistant for studying the clinical use of Alisma.