Increasing applications of multiwalled carbon nanotubes (MWCNT) lead to significant occupational exposure and potential health concerns. Toxicity of MWCNT should be carefully elucidated since the conventional (CON) method with fully immersed condition fails to mimic the air-liquid interface (ALI) in airways. Additionally, quantification of MWCNT in cells was a real challenge. Currently available ALI exposure devices are costly, posing problems to conducting in vitro evaluations for emerging nanomaterials. A novel system, consisting of a shaker fluidized-bed atomizer (SFA) and electrostatic shallow liquid interface (ESLI) exposure chamber, has been developed for investigating nanotoxicity of well-dispersed pristine-MWCNT (pMWCNT) and carboxylized-MWCNT (cMWCNT). After 24-h exposure, LDH, MCP-1, IL-1β, IL-6, and TNF-α releases were determined, and cell uptakes were quantified according to the molybdenum content in cells. Biological responses triggered by SLI exposure are obviously more sensitive compared with those caused by CON exposure at equivalent doses. Exposure dose-dependent release of LDH and IL-6 was highlighted in A549 cells, indicating higher cytotoxicity and inflammatory responses of cMWCNT attributed to its shorter length, smaller size, and higher cell uptake. Cell-associated dose-dependent release of LDH and IL-6 was highlighted in RAW264.7 cells, revealing the higher adverse health risk of pMWCNT due to frustrated phagocytosis and its much higher molybdenum content. These results suggest that inherent characteristics of cells and distinct physicochemical properties of pMWCNT and cMWCNT lead to either exposure dose-dependent or cell-associated dose-dependent responses. Notably, the SLI is superior to the CON exposure method and well suited for nanotoxicity assessment of different MWCNTs.