Layered heterometallic phosphates {Mn(H₂O)₄}₂Mn(H₂O)₂Ru₂(PO₄)₄(H₂O)₂ (1) with a new topology were constructed from Ru₂(PO₄)₄⁶⁻ and Mn²⁺ in the presence of anions as assisting reactants whose alkaline strength plays a key role in directing a different number of lattice water-intercalated structures. In the presence of CO₃²⁻ and SO₄²⁻ as assisting reactants, the assembling reaction in the aqueous solution at room temperature results in compounds 1·10H₂O and 1·4H₂O, respectively. Single-crystal X-ray diffraction analysis reveals that compounds 1·10H₂O and 1·4H₂O crystallize in orthorhombic space group Pbca and monoclinic space group P2₁/c, respectively. The layered structure of 1 is constructed by alternating Ru₂O₁₀ tetragonal dipyramid and MnO₆ octahedra bridged by PO₄ tetrahedra. The neutral heterometallic phosphate layers of 1 are separated by a different number of interlayer lattice water molecules, and hydrogen bonds are responsible for the neutral inorganic layer connection. Magnetism measurements show that compound 1·10H₂O exhibits a soft magnet behaviour ordering below 8.5 K with indirect hydrogen bonding between these ferrimagnetic layers, and a reentrant spin-glass-like transition is observed for compound 1·4H₂O, exhibiting two steps transition at 8.0 and 12 K, due to a strong competition between intralayer magnetic coupling and interlayer antiferromagnetic interactions mediated through the direct hydrogen bonding.