Thorium is a well-known radioactive and chemically toxic contaminant in the environment. The continuous exposure to thorium may cause an increased risk of developing lung and liver diseases as well as lung, pancreas, and bone cancer. Due to its use in nuclear industry and other industrial applications, thorium may be accidentally released to the environment from its mining and processing plants. In this work, we developed a rapid, real-time, and label-free nanopore sensor for Th detection by using an aspartic acid containing peptide as a chelating agent and tuning the electrolyte solution pH to control the net charges of the peptide ligand and its metal ion complex. The method is highly sensitive with a detection limit of 0.45 nM. Furthermore, the sensor is selective: other metal ions (e.g., UO, Pb, Cu, Ni, Hg, Zn, As, Mg, and Ca) with concentrations of up to 3 orders of magnitude greater than that of Th would not interfere with Thdetection. In addition, simulated water samples were successfully analyzed. Our developed computation-assisted sensing strategy should find useful applications in the development of nanopore sensors for other metal ions.