Mulberry anthocyanin extract (MAE) is a valuable natural pigment with potential applications in the food industry. However, its storage stability remains a challenge, as it is prone to degradation over time. To tackle this issue, the present study focuses on investigating the efficacy of utilizing whey protein isolate (WPI) and ferulic acid (FA) in combination at pH 6.3. The addition of FA reduced the ΔE values and the degradation of anthocyanin within MAE solution in the presence of WPI. Notably, the combination of WPI and FA exhibited a remarkable stabilizing effect on the MAE solution. Multi-spectroscopic analysis revealed the occurrence of non-covalent interactions mediated by hydrophobic interaction between β-lactoglobulin (β-LG) and cyanidin-3-O-glucoside (C3G) in the presence of FA, with improved binding affinity. While FA did not exhibit a copigmentation effect on the C3G solution, it enhanced the protective action of β-LG on the chromophoric structural form of C3G. Moreover, although the introduction of FA to the β-LG complex with C3G resulted in minor modifications to the secondary structure, in contrast to the binary complexes, its particle size increased. The molecular dynamics simulations also revealed that FA enhances the binding affinity between β-LG and C3G. These findings provide a foundation for enhancing the storage stability of anthocyanins and expanding the utilization of MAE pigment in the food industry.