The nuclear and magnetic structures of CaxSr2−xWMnO6 (x = 0.5, 1.0, 1.5) have been investigated by neutron diffraction at 295, 30 or 40 K, and 4 or 5 K. The compounds crystallized in the monoclinic symmetry with a space group P21/n. The nuclear structure consists of ordered WO6 and Mn2+O6 octahedral frameworks, with lattice constant a decreasing more rapidly than b with increasing Ca content. No structural change was found around the magnetic transition temperature, although the Mn octahedron below the magnetic order temperature exhibited a slightly compressed Jahn–Teller distortion (0.1–0.3 Å) along the c axis. A standard magnetic model was used to solve the magnetic structure, with the Mn magnetic moments ferromagnetically coupled along the a axis and anti-ferromagnetically coupled along the b and c axes, resulting in a magnetic propagation vector of k = (0,1/2, 1/2) and a magnetic superlattice of 1a × 2b × 2c. In each crystallographic cell, the Mn1–Mn2 atoms are antiferromagnetically configurated, compensating the total moment to zero by symmetry. A layer-type magnetism along the (111) crystallographic plane was confirmed to couple antiferromagnetically between these planes and ferromagnetically within them. The magnetic structure refinement confirmed an average Mn moment of 4.5 μB. Also, it reveals that the collinear magnetic Mn configuration has three possible spin orientations, namely, (with their standard deviation) [μx = (3.3 ± 0.4) μB, μy = (2.5 ± 0.3) μB, μz = (−0.7 ± 0.7) μB], [μx = (3.0 ± 0.4) μB, μy = (0.5 ± 0.2) μB, μz = (−2.8 ± 0.2) μB, and [μx = (−1.8 ± 0.4) μB, μy = (2.9 ± 0.2) μB, μz = (−2.4 ± 0.3) μB. The first configuration is estimated to be the ground state, while the other magnetic configurations are an optimum local value derived from the refinements. Combined with the density functional theory calculations, these experimental results confirm a high-spin state Mn2+ (d5) electron configuration.