We report cooperative magnetic orderings in a 6H-perovskite multiferroic system, Ba3HoRu2O9, via comprehensive neutron powder diffraction measurements. This system undergoes long-range antiferromagnetic ordering at TN1 ~ 50 K with a propagation wave vector of K1 = (0.5 0 0), a transition temperature much higher than the previously reported one at ~10 K (TN2). Both Ru and Ho-moments order simultaneously below TN1, followed by spin-reorientations at lower temperatures, demonstrating strong Ru(4d)-Ho(4f) magnetic correlation. Below TN1 another magnetic phase with a propagation wave vector K2 = (0.25 0.25 0) emerges and coexists with the one associated with K1, which is rarely observed and suggests complex magnetism due to phase competition in the magnetic ground state. We argue that the exchange-striction arising from the up-up-down-down spin structure associated with K2-wave vector below TN2 may be responsible for the small ferroelectric polarization reported previously in this compound.