This paper proposes a new class of mass or energy conservative numerical schemes for the generalized Benjamin-Ono (BO) equation on the whole real line with arbitrarily high-order accuracy in time. The spatial discretization is achieved by the pseudo-spectral method with the rational basis functions, which can be implemented by the Fast Fourier transform (FFT) with the computational cost $mathcal{O}( Nlog(N))$. By reformulating the spatial discretized system into the different equivalent forms, either the spatial semi-discretized mass or energy can be preserved exactly under the continuous time flow. Combined with the symplectic Runge-Kutta, with or without the scalar auxiliary variable reformulation, the fully discrete energy or mass conservative scheme can be constructed with arbitrarily high-order temporal accuracy, respectively. Our numerical results show the conservation of the proposed schemes, and also the superior accuracy and stability to the non-conservative (Leap-frog) scheme.