Free and active concentration of drug in the blood plays a vital role in the disease treatment. Binding of drug to serum albumin, an important transport protein in plasma, usually improves its aqueous solubility, stability and bioactivity. Brazilin (Bra) is a natural compound extracted from Caesalpinia sappan with numerous pharmacological applications, while the behavior of Bra in circulatory system is still unknown. Therefore, in the present work, we firstly examined the interaction of Bra with bovine serum albumin (BSA) using various spectroscopic and computer simulation techniques. The static quenching mechanism and moderate binding affinity (2.18 × 104 M−1 at 298 K) were obtained through fluorescence spectroscopic measurement. Thermodynamic analysis results indicated that hydrophobic interactions and hydrogen bonds played a major role in the binding process. Site marker competitive experiments and molecular simulation suggested that the probable Bra-binding position was located in subdomain IIA of BSA. UV–vis absorption, circular dichroism (CD) and dynamic light scattering (DLS) experiments suggested the conformational changes of BSA induced by Bra. Additionally, the potential of Bra to inhibit the formation of amyloid fibrils, in vitro, has also been analyzed. Thioflavin T (ThT) binding, 8-anilino-1-naphthalenesulfonic acid (ANS) binding, Congo red binding, DLS, CD, fluorescence microscopic image, atomic force microscopy (AFM), size-exclusion chromatography (SEC) and native gel-electrophoresis methods were used, and all confirmed the anti-amyloidogenic behavior of Bra. In short, our findings have provided some important insights into the binding mechanism of Bra with BSA, and would be helpful in designing suitable agents against amyloid diseases.