We compute three-body nuclear forces at short distances by using the nuclear matrix model of holographic QCD proposed in our previous paper with P. Yi. We find that the three-body forces at short distances are repulsive for (a) aligned three neutrons with averaged spins, and (b) aligned proton-proton-neutron/ proton-neutron-neutron. These indicate that in dense states of neutrons such as cores of neutron stars, or in Helium3/ tritium nucleus, the repulsive forces are larger than the ones estimated from two-body forces only.