Centrin, a member of calcium-binding proteins, is an essential component for microtubule-organizing center (MTOC). Lanthanide (Ln) ions can increase amounts, enhance stability and orderliness of microtubules which is an important component of cytoskeleton. To investigate the structural basis of the effect of Ln ions on orderliness of microtubules, we focused on the interactions between the isolated N-terminal domain of Euplotes centrin (N-EoCen) and Ln by some combined biophysical and biochemical methods. Our results suggest that Ln ions may bind to the canonical calcium binding sites on N-EoCen. Taking advantage of ligand competition, we first determined the metal-binding affinities of Nd(3+), Eu(3+), Gd(3+) and Tm(3+) with N-EoCen. Major changes of N-EoCen in secondary and tertiary structure are noted while Ln ions bind with N-EoCen through CD spectra and 2-p-toluidinylnaphthalene-6-sulfonate (TNS) fluorescence. N-EoCen exists in the form of monomer and dimer in the presence of Ln ions. These results can provide some insights into the structural basis of how Ln ions achieve biological effect in cell through the centrin protein.