Fe 4 Nb 2 O 9 was recently reported to be a new magnetoelectric material with two distinct dielectric anomalies located at T N ≈ 90 K for an antiferromagnetic transition and T str ≈ 77 K of unknown origin, respectively. By analyzing low-temperature neutron-powder-diffraction data, here we determined its magnetic structure below T N and uncovered the origin of the second dielectric anomaly as a structural phase transition across T str . In the antiferromagnetically ordered state below T N , both Fe1 and Fe2 magnetic moments lying within the weakly and strongly buckled honeycomb layers are arranged in a fashion that the three nearest neighbors are directed oppositely. Upon cooling below T str , the symmetry of crystal structure is lowered from trigonal P-3c1 to monoclinic C2/c, in which a weak sliding of the metal octahedral planes introduces a monoclinic distortion of ∼1.7 • . The magnetic structure is preserved in the low-temperature monoclinic phase, and the Fe magnetic moment increases from 2.1(1)μ B at 95 K to 3.83(4)μ B at 10 K assuming an equal moment configuration at Fe1 and Fe2 sites. The magnetic point group and linear magnetoelectric tensor at each temperature region are determined. From a symmetry-related tensor analysis, the microscopic origins of the magnetoelectric effects between T N and T str are proved to be spin-current and d-p hybridization mechanisms.