To investigate the aberrant expression of nuclear matrix proteins in human gastric cancer cells before and after hexamethylene bisacetamide (HMBA) treatment. Proteomics analysis of differential nuclear matrix proteins was performed by two dimensional electrophoresis polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The expression levels of three nuclear matrix proteins were further confirmed by Western blotting and their locations in nuclear matrix filament were observed by quantum dots-based immunofluorescence. Proteomics analysis showed that 43 protein spots were significantly changed due to HMBA treatment. Fifteen proteins were identified in the HMBA-induced differentiation of gastric tumor cells. Eight proteins spots were down-regulated while seven were up-regulated. Among these proteins, prohibitin, nucleophosmin and hnRNP A2/B1 were significantly decreased in HMBA-treated human gastric cancer cells, and their locations in nuclear matrix were altered by HMBA. Our results proved the alteration of specific nuclear matrix proteins during the differentiation of human gastric cancer cells. And the aberrant expressions of nuclear matrix proteins were of significance in revealing the regulatory mechanism of tumor cell proliferation and differentiation. The aberrant expressions and intracellular redistributions of nuclear matrix proteins before and after HMBA treatment indicated that nuclear matrix proteins play a pivotal role in the differentiation of gastric cancer cells.