In this study, new bisphosphonate-functionalized ionic organic crystals (IOCs) were developed by π-π and ionic interactions with the high oxygen content of the phosphonic acid group. Meanwhile, this novel material achieved an extremely high selectivity of Th adsorption with a saturation adsorption capacity of 426 mg/g. In addition, the heat resistance (400 °C) and the recyclability (more than five cycles) make the IOCs economical for their extraordinary stability. Moreover, we use single-crystal X-ray diffraction to determine the monomer connections and the ionic bonds. We used kinetic fitting and X-ray photoelectron spectroscopy testing to explain the adsorption mechanism, which reveals a monolayer adsorption process with a distinct O-Th bond post-adsorption. This study not only gave an example to develop new ionic single crystals based on different functional groups but also expanded the potential application to use these new types of nanomaterials.