The physicochemical properties of nanomaterials play crucial roles in determining their biological effects. Agglomeration of nanomaterials in various systems is a common phenomenon, however, how agglomeration affects the biological consequence of nanomaterials has not been well investigated because of its complexity. Herein, we prepared variable sized agglomerates of oxidized multi-walled carbon nanotubes (O-MWCNTs) by using Ca(2+) and studied their cellular uptake and cytotoxicity in HeLa cells. We found the altered property of O-MWCNTs agglomerates could be controlled and adjusted by the amount of Ca(2+). Agglomeration remarkably facilitated the cellular uptake of O-MWCNTs at the initial contact stage, due to the easy contact of agglomerates with cells. But agglomeration did not induce evident cytotoxicity when the concentration of O-MWCNTs was less than 150μg/mL. That was assayed by cell proliferation, membrane integrity, apoptosis and ROS generation. This study suggests us that the biological behaviors of nanomaterials could be altered by their states of agglomeration.