Pharmacophore‐based virtual screening (VS) has emerged as an efficient computer‐aided drug design technique when appraising multiple ligands with similar structures or targets with unknown crystal structures. Current pharmacophore modeling and analysis software suffers from inadequate integration of mainstream methods and insufficient user‐friendly program interface. In this study, we propose a stand‐alone, integrated, graphical software for pharmacophore‐based VS, termed ePharmer. Both ligand‐based and structure‐based pharmacophore generation methods were integrated into a compact architecture. Fine‐grained modules were carefully organized into the computing, integration, and visualization layers. Graphical design covered the global user interface and specific user operations including editing, evaluation, and task management. Metabolites prediction analysis with the chosen VS result is provided for preselection of wet experiments. Moreover, the underlying computing units largely adopted the preliminary work of our research team. The presented software is currently in client use and will be released for both professional and nonexpert users. Experimental results verified the favorable computing capability, user convenience, and case performance of the proposed software. The pharmacophores are efficiently generated according to two different inputs, the ligand and the protein. The top n small molecules with the best matches (highest scores) are virtually screened through PharmFit algorithm from the small molecule database. The sorted small molecules and metabolites prediction are visualized for intuitive understanding and further analysis. Well‐designed user interface conveniently assists users to interactive operations including editing, evaluation and task management.