Ureidopyrimidone (UPy) is an important building block for constructing functional supramolecular polymers and soft materials based on their characteristic quadruple hydrogen bonds. While the evidence from the single-crystal X-ray diffraction data for the existence of linear hydrogen bonding has still been absent up to now. To obtain the crystals of UPy-containing molecules with high quality, enhanced rigidity and crystallinity are expected. Herein, an inorganic Anderson–Evans type cluster [Mn(OH)6Mo6O18]3−, which can provide suitable stiffness and charge, is used as a linker to covalently anchor two UPy units. The prepared organic–inorganic polyanion with three negative charges has a linear architecture, which is prone to form an infinite one-dimensional structure based on the supramolecular forces. The results indicate that the combination models of UPy units can be conveniently modulated by organic counter cations with different sizes, and therefore three unreported models are observed under various conditions. The present study gives a unique understanding of the intermolecular interactions in UPy-based supramolecular polymers and also provides a simple tuning method, which benefits the construction of functional materials and the adjustment of their properties.