Co4Ta2O9 exhibits a three-dimensional magnetic lattice based on the buckled honeycomb motif. It shows unusual magnetoelectric effects, including, in particular, the sign change and nonlinearity. These effects cannot be understood without the detailed knowledge of the magnetic structure. Herein, we report neutron diffraction and direction-dependent magnetic susceptibility measurements on Co4Ta2O9 single crystals. Below 20.3 K, we find a long-range antiferromagnetic order in the alternating buckled and flat honeycomb layers of Co 2+ ions stacked along the c-axis. Within experimental accuracy, the magnetic moments lie in the ab-plane. They form a noncollinear antiferromagnetic structure with a tilt angle of ∼ 14 • at 15 K in the buckled layers, while the magnetic moments in each flat layer are collinear. This is directly supported by a finite (0, 0, 3) magnetic Bragg peak intensity, which would be absent in the collinear magnetic order. The magnetic space group is C2 /c, which is different from the one previously found in powder neutron diffraction, as well as in the isostructural Co4Nb2O9. The revised magnetic structure successfully explains the major features of the magnetoelectric tensor within the framework of the spin-flop model.