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Abstract The selective separation of thorium from rare earth elements and uranium is a critical part of the development and application of thorium nuclear energy in the future. To better understand the role of different N sites on the selective capture of Th(IV), we design an ionic COF named Py-TFImI-25 COF and its deionization analog named Py-TFIm-25 COF, both of which exhibit record-high separation factors ranging from 102 to 105. Py-TFIm-25 COF exhibits a significantly higher Th(IV) uptake capacity and adsorption rate than Py-TFImI-25 COF, which also outperforms the majority of previously reported adsorbents. The selective capture of Py-TFImI-25 COF and Py-TFIm-25 COF on thorium is via Th-N coordination interaction. The prioritization of Th(IV) binding at different N sites and the mechanism of selective coordination are then investigated. This work provides an in-depth insight into the relationship between structure and performance, which can provide positive feedback on the design of novel adsorbents for this field.