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The paper constructs a conservative Fourier pseudo-spectral scheme for some conservative fractional partial differential equations. The scheme is obtained by using the exponential time difference averaged vector field method to approximate the time direction and applying the Fourier pseudo-spectral method to discretize the fractional Laplacian operator so that the FFT technique can be used to reduce the computational complexity in long-time simulations. In addition, the developed scheme can be applied to solve fractional Hamiltonian differential equations because the scheme constructed is built upon the general Hamiltonian form of the equations. The conservation and accuracy of the scheme are demonstrated by solving the fractional Schrödinger equation.