Abstract The characteristics of modulated internal solitary waves (ISWs) under the influence of one mesoscale eddy pair in the Luzon Strait, involving one anticyclonic eddy (AE) and one cyclonic eddy (CE) induced by the Kuroshio intrusion, were investigated using a nested high-resolution numerical model in the northeastern South China Sea (SCS). The presence of mesoscale eddies greatly impacts the nonlinear evolution of type-a and type-b ISWs. The eddy pair contributes to distinct wave properties and energy evolutions. Compared to type-b waves, type-a waves display more pronounced modulatory characteristics with a larger spatial scale. CE currents and horizontal inhomogeneous stratification are crucial in modulating the wave behaviors, which induce extremely large-amplitude depression ISWs. The AE thereafter yields retardation effects on the wave energy evolution. The average depth-integrated available potential and kinetic energy showed relative growth rates of −66.12% and −46.07%, respectively, for type-a waves, and −24.26% and −20.15%, respectively, for type-b waves along the propagation path up to the AE core. The deformed and distorted ISW crest lines propagating further northward exhibit a more dramatic shoaling evolution. The maximum total energies of type-a and type-b waves at the north station are approximately 13.5 and 3.5 times, respectively, greater than those at the south station on the continental shelf of the Dongsha Atoll. This work provides essential insights into modulated ISW dynamics under the mesoscale eddy pair within the northeastern SCS deep basin.