Thaumatin-like proteins (TLP), existing in various fruits, have allergenic and pro-inflammatory activities. The current research attempts to reduce the pro-inflammatory activity of litchi TLP (LcTLP) through high hydrostatic pressure (HHP). This study demonstrated that HHP (250–500 MPa, 5–10 min) was a potential technique to reduce the pro-inflammatory activity of LcTLP, which was attributed to the irreversible destruction of the active domain, ie., V-cleft. SDS-PAGE showed no change in the protein profile. Continuous HHP treatment promoted LcTLP unfolding and then reassembling (400 MPa was the transition pressure), and the content of β-sheets decreased from 35.4% to 31.1%. HHP treatment could mitigate inflammatory responses of LcTLP, as confirmed by ELISA and western blot. Molecular dynamics simulations showed significant changes in the residue network under HHP, thereby affecting the V-cleft. These findings provide a theoretical explanation and structural insights into the HHP-induced reduction of pro-inflammatory activity of LcTLP.