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The primary objective of this study was to investigate the binding of buddleoside to bovine serum albumin (BSA) by different analytical techniques. The analytical principles of affinity capillary electrophoresis (ACE) and fluorescence spectroscopy used in the experiments were different. Mobility (M) that is independent of viscosity of the operating buffer and voltage was chosen to eliminate the effects of electroosmotic flow (EOF) in ACE and was applied to estimate the binding constant Ka. The quenching constant Ksv, binding site number n and binding constant Kb were provided by the fluorescence quenching method. After data analysis of the fluorescence quenching process, it can be seen that the quenching of BSA by buddleoside is a static quenching method. The binding constants between buddleoside and BSA obtained from ACE and fluorescence spectra were 1.218×105 and 1.1915×105, respectively. According to the thermodynamic parameters of ΔG, ΔH and ΔS, it can be inferred that Van Der Waals force and hydrogen bonding force exist in the interaction between buddleoside and BSA. This study can provide a reference for the study of the transport and function mechanism of buddleoside in vivo.