Disturbance of the homeostatic balance of cell growth and cell death can lead to cancerogenesis, as designated by the over-expression of anti-apoptotic genes observed in lymphomas. B-cell lymphoma 6 at BTB domain (BCL6BTB) is an oncoprotein upregulated in leukemia, amplified in breast cancer cell and plays in a broad spectrum in oncogenic various types of cancer. Therefore, in this article we report a molecular docking research of a series of chalcone-thiourea hybrid molecules which further can be used as candidate of anticancer agent under inhibition of BCL6BTB mechanism. Program DOCK 6 was used for the docking experiment. The molecular structure of protein BCL6BTB was used as the target protein (PDB: 6CQ1). Standard residue charges were calculated using the force field ff4SB method, while nonstandard residue charges were calculated using the Gasteiger method. The docking experiment revealed that compound (E)-1-(4-(3-oxo-3-(3,4,5-trimethoxyphenyl) prop-1-en-1-yl) phenyl) thiourea showed better property can be used as anticancer candidate for para thiourea isomer, whereas compound (E)-1-(3-(3-oxo-3-phenylprop-1-en-1-yl) phenyl) thiourea is the candidate for meta thiourea isomer. In brief, para thiourea isomer exhibited better anticancer activity than meta thiourea isomer.