In this study, a homogeneous polysaccharide, named YDOP-1 was isolated form Dendrobium officinale using hot water extraction and ethanol precipitation method. YDOP-1 was characterized to be a typical O-acetyl-glucomannan with the molecular wight was 13,456 Da. Cell viability and colony forming assay showed that YDOP-1 possess moderate anti-gastric cancer effects. In order to further improve the anti-gastric cancer effects of YDOP-1, a selenium modification on YDOP-1 was performed. Energy dispersive spectrometer (EDS) and X-ray photoelectron spectroscopy (XPS) analysis demonstrated that the Se was successfully introduced into YDOP-1 by forming SeO bonds. Se modification significantly enhanced the anti-gastric cancer effects of YDOP-1, which could effectively inhibit the proliferation of MGC-803 cells via suppressing colony and inducing apoptosis by regulating the apoptosis proteins of Bax, Bcl-2, and Caspase-7. Our results indicated that the Se modified O-acetyl-glucomannan, YDOP-Se, was expected to be useful in the biomedicine field for the gastric cancer treatment.