Biomedical application potentials of carbon nanotubes-based materials have been investigated intensively in recent years; however, characterization and metrology are still facing great technical challenges when the materials are intended to be used as carriers for therapeutics in aqueous solutions. Systematic characterization on the dispersing carbon nanotubes is urgently required and therefore of significance. In this paper multiwalled carbon nanotubes (MWCNTs) with different average lengths or with different oxidation degrees were dispersed in water and characterized systematically by applying UV spectroscopy, SEM, DLS, TGA, XPS, and FTIR. In particular, the characteristic absorption of the carbon nanotubes was analyzed using resolution-fitting technique to establish relations of wavelength and absorption intensity to the size distribution and surface chemistry. Results indicated that the absorption spectra of MWCNTs could reflect the variation of surface chemistry and length distribution of carbon nanotubes dispersed in water by combining with the other measurements. A vascular endothelium cell line was taken as a model to figure out association between physicochemical features and cytotoxicity of the carbon nanotubes. It was showed that the multiwalled carbon nanotubes with different oxidation degrees and similar length distribution exhibited different interaction files to the cells proliferation in a manner of time dependence and concentration dependence.