By using a mixed-ligand approach, a new Cu(II)-based coordination polymer, whose chemical formula is [Cu2(DPFE)(oba)2]n (1), was synthesized through the reaction of the DPFE ligand with Cu(II) salts in the presence of V-shape polycarboxylate acid H2oba [DPFE = 2,7-di(pyridin-4-yl)-9H-fluorene, H2oba = 4,4′-oxydibenzoic acid]. The as-prepared complex 1 was fully determined via single crystal X-ray diffraction, powder X-ray diffraction, elemental analysis, Fourier transform infrared spectroscopy, and thermogravimetric analysis. Results from structural determination showed that complex 1 revealed a 3D framework structure featuring a twofold jsm interpenetrated network. The protective capability of the compound on DVT was evaluated, and the specific mechanism was discussed. The compound could reduce the weight and length of the thrombus in the inferior vena cava. However, the inflammatory response in the vascular endothelial cells was significantly declined after treatment of the compound. Results from molecular docking simulation indicated that all the polar atoms on the complex could form binding interactions to the C-reactive protein (CRP).