HDAC-IN-99 is a histone deacetylase (HDAC) inhibitor with an IC50 of 37.73 nM, and it exhibits potent inhibitory activity against HDAC1 (IC50 = 48.09 nM), HDAC2 (IC50 = 300.28 nM) and HDAC6 (IC50 = 9.16 nM). HDAC-IN-99 inhibits the enzymatic activity of HDAC and exerts broad-spectrum antiproliferative activity in various cancer cell lines. HDAC-IN-99 induces S-phase cell cycle arrest and apoptosis in colon cancer cells, increases the acetylation levels of histone H3, histone H4 and α-tubulin, and upregulates the expression of p21 as well as the cleavage of caspase-3. HDAC-IN-99 displays antitumor activity in colon cancer xenograft models. HDAC-IN-99 can be used for the research of colon cancer.