This work aims to investigate the preparation, characterization and interaction mechanism between soy protein nanogel and red raspberry anthocyanin (AC) at acidic environment. Soy protein nanogel was produced using a heat-induced aggregation method to fabricate complex of soy protein nanogel and AC. This method produced complex with nano-scale size ranged from 95.16 ± 1.5 to 137.30 ± 1.5 nm. Fluorescence quenching suggested that AC could effectively quench the fluorescence intensity of soy protein nanogel by static quenching, and the number of AC binding sites per protein molecule (n) was close to 1.0. The binding constant (Ka) was 1.572 × 104 L/M−1 at 298 K, indicating a strong binding between AC and soy protein nanogel. The results obtained from FTIR, UV–vis, and CD analysis confirmed that AC altered the secondary and tertiary structure of soy protein nanogel. Simulated docking results indicated that the binding between AC and soy protein was mainly following the hydrogen bonding and hydrophobic interactions. DSC results confirmed the interaction between soy protein nanogel and AC as evidenced by the decrease of soy protein nanogel thermal stability from 90.3 to 87.5 °C for soy protein nanogel with AC. Moreover, the band intensity of soy protein nanogel decreased with the increase of AC concentration observed through SDS PAGE. These results may help in a better understanding of the interaction between AC and soy protein nanogel and could be interestingly for the application of soy protein nanogel with AC in functional foods.