The spectral energy distributions (SEDs) of the high energy neutrino emitted from the accretion flows are still highly uncertain, because the global structure of the accretion flow can affect the neutrino SEDs. We have computed high energy neutrino SEDs by using three-dimensional general relativistic magnetohydrodynamic (GRMHD) simulations data of a magnetized accretion flow around a spinning black hole. The SEDs of the nonthermal protons are calculated by solving the Fokker-Planck equation in the rest frame of the tracer-particles of protons. We assume the effects of the turbulent accelerations with the hard-sphere approximation and compression/expansion of the fluid elements. For the hadronic processes, we consider the effects of the $pp$ collisions and subsequent high energy neutrino emissions taking into account the effect of the gravitational redshift. We have found that the neutrino SED become flatter than the previous 1 zone models because of the superposition of the neutrino SED emerged from the different position of the accretion flows.