We present a generalized non-Hermitian equation of motion (nH-EOM) to go beyond standard trajectory surface hopping dynamics. The derivation is based on the Born-Huang expansion of the total wave function and the polar representation of the nuclear factor. The nH-EOM contains two additional terms, a skew symmetry term iΓ with dissipation operator Γ to account for decoherence, and a kinetic-energy renormalization term to account for phase shifts, without destroying the invariance to the choice of representation. Numerically, the nH-EOM can still be solved efficiently using a semiclassical approximation in the framework of Tully's fewest-switches surface hopping (FSSH) algorithm. Applications to model Hamiltonians demonstrate improved performance over the standard FSSH approach, through comparison to exact quantum results.