There is a growing consumption on puffer fish-based food since this species contains high nutritional properties in terms of high protein and low fat values. However, this is hampered by the tough texture of puffer muscle. In this study, a simple but robust strategy to improve the tenderness of puffer muscle by papain treatment of different concentration (60, 80, 100, 120 and 140 U/mL) was developed. Results showed that the shear force and the hardness of fish muscle decreased significantly with increasing papain concentration, indicating improved tenderness of fish muscle. Protein patterns from SDS-PAGE confirmed that the papain-treated muslces had increasing degrees of degradation with faded myosin heavy chain (MHC) band and actin band as well as an increasing amount of low molecular weight pepeptides around 25–35 kDa. This may associated with the loss of one major protein denaturation peak as revealed by differential scanning calorimetry (DSC). Conformational characterization showed that the relative content of α-helix decreased, while irregular coil structure increased with increasing papain concentration. These results suggested puffer myofibril proteins, mainly myosin and actin were hydrolyzed into low molecular peptides with more disorder structures, which might be responsible for the improved tenderness.