The effects of whey protein (WP) and bovine serum albumin (BSA) on the thermal stability of betanin (Bt) at different temperatures were investigated. Fluorescence spectroscopy, circular dichroism, and Fourier transform infrared spectroscopy were used to study the interaction between WP/BSA and Bt. The results showed that WP and BSA inhibited the degradation of Bt content and the protection provided with WP was better than with BSA. Additionally, the change of pH also affected the thermal degradation of Bt. The half-life (t1/2) of the compound was the longest at pH 5.0, and the t1/2 of Bt-WP was up to 2.99 h. The fluorescence analysis showed that Bt led to a static quenching of WP/BSA. Further, the interaction was a spontaneous process with electrostatic interactions being the main force. Synchronous fluorescence spectra presented alterations in microenvironment of Trp and Tyr residues of WP/BSA, respectively, upon interaction with Bt. Circular dichroism and Fourier transform infrared spectroscopy analysis indicated that characteristic peak positions of amide I, II band and the secondary structures of WP/BSA was changed upon conjugation with Bt.