This paper considers the fractional coupled nonlinear Schrödinger equation with high degree polynomials in the energy functional that cannot be handled by using the quadratic auxiliary variable method. To this end, we develop the multiple quadratic auxiliary variable approach and then construct a family of structure-preserving schemes with the help of the symplectic Runge-Kutta method for solving the equation. The given schemes have high accuracy in time and can both inherit the mass and Hamiltonian energy of the system. Ample numerical results are given to confirm the accuracy and conservation of the developed schemes at last.