Three phosphonates coordination polymers containing different metal ions with the molecular formula C15H32N3M2O16P [M = Ni (PN1) and Co (PC1)] and C30H50N6Ni2.67Co1.33O27P2 (PNC) were prepared by mild hydrothermal synthesis at 100 °C for 48 h. All 3 phosphonates are composed of two different ligands: N-(phosphonomethyl)iminodiacetate (pmida) and 4,4′-bipyridine (4,4′-bpy). The structures of the materials were elucidated via single crystal X-ray diffraction techniques which show all compounds have the similar hybrid three dimensional (3-D) super structures via hydrogen bonds in triclinic symmetric and P-1 space group. The morphologies of the particles were characterized by SEM showing the irregular block shape. The electrochemical properties of 3 phosphonates were studied by cyclic voltammetry (CV), alternating current impedance spectroscopy (EIS) and constant current charge-discharge measurements. The discharge capacity remains to 288.1 mAh/g at 100th cycle with a current density of 50 mA/g and still behaves a growing trend. The CV data shows the large range of 0–10 V with the reduction peak at 4.7 V suggest that PC1 may be suitable for preparing high voltage lithium ion batteries (Libs). The performance of PC1 indicate promising for potential negative electrode material for Libs.