Alzheimer’s disease (AD) is also known as neurodegenerative disease, which normally causes 60–70% of dementia. There are many genetic and environmental risk factors associated with its development. The strongest genetic risk factor occurs by apolipoprotein E (apoE). Another type of risk factor may include high blood pressure, clinical depression, and head injury. In 2015, there were 29.8 million people affected worldwide by AD. Women get at risk more often than men. The present study was to inhibit the expression of apoE by dihydrohelenalin (DH) with the help molecular docking for the treatment of AD. The molecular docking method was performed after the screening of molecules and selecting the ligands which can inhibit and target the proteins. apoE (Protein Data Bank [PDB] ID 1GS9) protein was targeted through seven ligands compound and the best ligand was selected for further molecular docking and modeling tools. Thus, screening showed DH (with the binding affinity of −5.3 kcal/mol) as a ligand molecule that may inhibit apoE. DH has the highest binding properties. Thus, it may be used further used for the treatment of AD. The DH may be the beneficial drug for the treatments of AD in future studies after in vitro and in vivo studies.