Water-solubilized quantum dots have led to a promising application in cellular labeling and biological imaging. The physicochemical properties of water-solubilized quantum dots, particularly in a physiological environment, are strongly dependent on their size. In this paper, we systematically studied the stability of mercaptosuccinic acid-coated CdTe quantum dots (MSA-QDs) of about 2.3 and 5.4 nm diameters in various buffers with different pH values and under laser irradiation by fluorescence spectroscopy. It was found that larger MSA-QDs showed better stability. Size-dependent uptake of MSA-QDs by living HeLa cells was further investigated by confocal microscopy. In phosphate buffer solution, the larger MSA-QDs entered the cells mainly by endocytosis, and part of the smaller ones entered the cells by passive penetration. In cell culture medium, their uptake pathways could be changed due to the changes of their surface properties. The cytotoxicity of smaller and larger MSA-QDs was significantly decreased due to the adsorption of some biological components in the cell culture medium on the nanoparticles surface.