•Solvents, temperature and reactants ratio play key roles in the self-assembling.•{Ru2(CO3)4}n3n− layers linked by Mn2+ in a trans manner form pillared layer structure.•Ferromagnetic coupling results in glassy behavior ordering below 4.5 K.The self-assembly of Ru2(CO3)43− and Mn2+ ions in aqueous solution yields a new heterometallic carbonate complex K4[Mn(H2O)4{Ru2(CO3)4}2]·4H2O (1). X-ray diffraction studies on molecular structure reveal that complex 1 is consisted of undulate square-grid layers {Ru2(CO3)4}n3n−, and half of Ru2 dimers between the neighboring layers are linked by Mn(H2O)42+ in a trans manner forming a pillared layer structure of {Mn(H2O)4[Ru2(CO3)4]2}n4n−. Magnetism measurement indicates that complex 1 shows a spin glass behavior ordering below 4.5 K.Half of Ru2 dimers between the neighboring layers {Ru2(CO3)4}n3n− are linked by Mn(H2O)42+ in a trans manner forming a pillared layer structure of {Mn(H2O)4[Ru2(CO3)4]2}n4n−. Magnetism measurement indicates that it shows a spin-glass behavior ordering below 4.5 K.