A new type of phenanthroline carboxamide(DAPhen)-phosphate ester ligand (L1/L2) was synthesized for the selective separation of U(VI) over Th(IV). Liquid-liquid extraction experiments showed that the introduction of phosphate ester could increase the extraction ability of ligands for U(VI), especially L2, which showed high selectivity for the separation of U(VI) over Th(IV). The slope analysis indicated that L1 could form 1:1 and 1:2 complexes with U(VI) and 1:1 complexes with Th(IV). NMR titration revealed that the DAPhen unit of ligands combined with one U(VI) to form 1:1 complexes, and then the phosphate ester unit of the 1:1 complexes further combined with another U(VI) to form 1:2 complexes. Ligands provide only the DAPhen unit to Th(IV) to form 1:1 complexes. The crystal structures found 1:2 complexes of L1 and U(VI), 1:1 complexes of L2 and U(VI), and 1:1 complexes of L1 and Th(IV). The larger stability constant (log β) of the 1:1 complexes of L2 with U(VI) than that of the 1:1 complexes of L1 with U(VI) showed that the binding ability of U(VI) with the DAPhen unit of L2 is stronger than that of U(VI) with the DAPhen unit of L1. This study provides new ideas for designing extractants with excellent properties.