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.