This study aimed to compare and analyze the relative antioxidant and anticancer effects of Bokhaejeong Ganjang (BG) manufactured by adding sulfur duck essence with those of Seomoktae Ganjang (SG) and Commercial Ganjang (CG) on HT-29 human colon cancer cells. The analysis of the physicochemical properties (pH value, acidity, and salinity) revealed that BG and SG had a higher pH and salinity, and lower acidity than CG. In addition, as the treatment concentration increased, the total flavonoid content and 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity markedly increased, and were found to be significantly higher than those of CG. The effect of BG on the growth of HT-29 colon cancer cells was investigated through a 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay, and the mRNA expression levels of factors related to cell cycle arrest and apoptosis were determined. The results confirmed that the growth inhibitory effect of BG on HT-29 cells increased in a concentration-dependent manner. The mRNA expressions of genes related to cell cycle arrest p53 and p21, and pro-apoptosis factors, namely BIM, BAK, caspase 9, and caspase 3, were significantly up-regulated. In addition, the mRNA expression of BCL-2, an anti-apoptosis factor, was decreased. These results indicated that BG with bamboo salt, sulfur duck essence, and Seomoktae showed a high flavonoid content and DPPH free radical scavenging ability, and an anticancer effect in colon cancer cells by suppressing the proliferation of HT-29 cancer cells via the regulation of genes related to cell cycle and apoptosis.