Recognizing of binding mechanisms between drugs and carrier proteins is basic for us to understand the pharmacokinetics and pharmacodynamics of them. In this research, the anticancer activities of a binuclear complex [Co(dipic)2Ni(OH2)5]·2H2O (dipic = dipicolinate) against MDA-MB-231 cell lines were studied. Results of MTT assay and flow cytometry analysis revealed that above complex can induce the cytotoxicity and the apoptosis in breast cancer cell lines. So, this complex was selected to investigate its binding to human serum albumin (HSA) and bovine β-lactoglobulin (βLG) by spectroscopic methods (UV–visible, fluorescence and FT-IR) along with molecular docking technique. The fluorescence data showed Co-Ni complex quench the fluorescence of both proteins by a static quenching mechanism and HSA has stronger binding affinity toward Co-Ni complex than βLG. The binding constant (Kb), number of binding sites (n) and thermodynamic parameters were calculated and showed that the Co-Ni complex binds to protein (HSA and βLG) through hydrogen bonding and van der Waals forces with one binding site. The results of UV–visible measurements indicated that the binding of above complex to HSA and βLG may induce conformational and micro-environmental changes of studied proteins. Protein–ligand docking analysis confirmed that the Co-Ni complex binds to residues located in the subdomain IIA of HSA and site II of βLG.