In this paper, we introduce fully discrete Fourier-Spectral numerical scheme to solve the nonlocal Cahn–Hilliard equation coupled with Navier–Stokes/Darcy equations, which represent a phase-field model for two-phase incompressible flow in either the free flow regime or a Hele-Shaw cell. The proposed scheme achieves full decoupling while maintaining linearity and energy stability through a combination of the Scalar Auxiliary Variable (SAV) method, which discretizes the nonlinear potential, and the “Zero-Energy-Contribution” (ZEC) method, which handles the coupled nonlinear advective/surface tension terms. The efficiency of this scheme is attributed to its linear decoupling structure and the fact that it requires only a few elliptic equations with constant coefficients to be solved at each time step. We rigorously establish the scheme’s unconditional energy stability. Further, some numerical simulations are provided in both 2D and 3D to show its effectiveness, including its accuracy, stability, and efficiency.