Materials and datasets used in "Designing Combinational Herbal Drugs Based on Target Space Analysis" are stored in this repository Additional file 1 (Target space analysis of TOM formula), additional file 2 (SWT formula-target association), additional file 3 (Drug Module 1-target association), and additional file 4 (Drug Module 2-target association), are found in the Github repository. Additional file 1 (Microsoft Excel Comma Separated Values File, .csv) shows the target space analysis result between the TOM formula and small-molecule drugs. In the current study, we analyzed 10 formulas known to treat Anxiety, 10 formulas known to treat Diabetes mellitus, 7 formulas known to treat Epilepsy, 6 formulas known to treat Hypertension, 6 formulas known to treat Obesity, and 7 formulas known to treat Schizophrenia. Additional file 2 (Microsoft Excel Worksheet, .xlsx) shows SWT formula-target association. We provided SWT formula-herb-compound-target associations. Additional file 3 (Microsoft Excel Worksheet, .xlsx) shows Drug Module 1-target associations. Drug Module 1 is a set of small-molecule drugs known to treat Women’s diseases such as climacteric syndrome, menstrual discomfort, and other estrogen-related diseases. Additional file 4 (Microsoft Excel Worksheet, .xlsx) shows Drug Module 2-target associations. Drug Module 2 is a set of small-molecule drugs known to treat the side effects of Drug Module 1.