Metabolites affect the binding mechanism between parent drug and transport protein. The effects of the metabolite nicotinamide (NTA) on the interaction mechanism of the antihyperlipidemic drug nicotinic acid (NA) with bovine serum albumin (BSA) were investigated through fluorescence spectroscopy, UV–Vis spectroscopy and FT-IR spectroscopy along with molecular docking. The fluorescence quenching results revealed that the NA/NTA bound to BSA in 1:1 stoichiometry with binding constants of Kb (NA-BSA) = 2.19 × 103 L·mol−1 and Kb (NTA-BSA) = 5.82 × 103 L·mol−1, respectively. The results of thermodynamic experiment (ΔH, ΔS and ΔG) showed that NA bound spontaneously with BSA through entropy driven hydrophobic interaction. The binding of NA/NTA caused conformational changes in BSA molecule, as proved by FT-IR spectroscopy, UV–Vis spectroscopy and synchronous fluorescence spectroscopy. The site marker experiment and molecular docking suggested that NA/NTA located in site I of BSA. The presence of metabolites did not significantly change the effect of sodium on the conformation of BSA, but increased the binding constant of NA and BSA.