Field-dependent magnetic structure of a layered Dirac material EuMnBi$_2$ was investigated in detail by the single crystal neutron diffraction and the resonant x-ray magnetic diffraction techniques. On the basis of the reflection conditions in the antiferromagnetic phase at zero field, the Eu moments were found to be ordered ferromagnetically within the $ab$ plane and stacked antiferromagnetically along the $c$ axis in the sequence of up-up-down-down. Upon the spin-flop transition under the magnetic field parallel to the $c$ axis, the Eu moments are reoriented from the $c$ to the $a$ or $b$ directions forming two kinds of spin-flop domains, whereas the antiferromagnetic structure of the Mn sublattice remains intact as revealed by the quantitative analysis of the change in the neutron diffraction intensities. The present study provides a concrete basis to discuss the dominant role of the Eu sublattice on the enhanced two-dimensionality of the Dirac fermion transport in EuMnBi$_2$.