A coupled system of fractional order Gross-Pitaevskii equations is under consideration in which the time-fractional derivative is given in Caputo sense and the spatial fractional order derivative is of Riesz type. This kind of model may shed light on some time-evolution properties of the rotating two-component Bose¢ Einstein condensates. An unconditional convergent high-order scheme is proposed based on L2-1σ finite difference approximation in the time direction and Galerkin Legendre spectral approximation in the space direction. This combined scheme is designed in an easy algorithmic style. Based on ideas of discrete fractional Grönwall inequalities, we can prove the convergence theory of the scheme. Accordingly, a second order of convergence and a spectral convergence order in time and space, respectively, without any constraints on temporal meshes and the specified degree of Legendre polynomials N. Some numerical experiments are proposed to support the theoretical results. © 2023 the Author(s).