Due to the maneuver and overload requirements of aircraft, it is inevitable that supersonic fins experience high angles of attack (AOAs) and viscous effects at high altitudes. The local piston theory with viscous correction (VLPT) is introduced and modified to account for the 3-dimensional effect. With the contribution of the explicit aerodynamic force expression and enhanced surface spline interpolation, a tightly coupled state-space equation of the aeroelastic system is derived, and a flutter analysis scheme of relatively small computational complexity and high precision is established with a mode tracking algorithm. A wind tunnel test conducted on a supersonic fin confirms the validity of our approach. Notably, the VLPT predicts a more accurate flutter boundary than the local piston theory (LPT), particularly regarding the decreasing trend in flutter speed as AOA increases. This is attributed to the VLPT’s ability to provide a richer and more detailed steady flow field. Specifically, as the AOA increases, the spanwise flow evolves into a gradually pronounced spanwise vortex, yielding an additional downwash and energizing the boundary layer, which is not captured by LPT. This indicates that the precision of LPT/VLPT significantly depends on the accuracy of steady flow results.