The extraction and separation of actinide over lanthanide elements is a key step in the spent fuel reprocessing process, which involves a variety of actinides with different valence states. The phenanthroline phosphonate (POPhen) extractants have a strong ability to extract trivalent actinides over lanthanides from highly acidic HNO3 solution with good separation ability of An(III) over Ln(III). However, the extraction properties and complexation mechanism of POPhen extractants for high-valence actinides have yet to be studied. In this work, U(VI) and Th(IV) were selected as representatives of high-valence actinides to systematically study the extraction effect and complexation mechanism of C2-POPhen and C4-POPhen with them. The results showed that POPhen extractants had excellent coordination and extraction ability for U(VI) and Th(IV) under highly acidic nitrate conditions. The extraction capacity of C4-POPhen was stronger than that of C2-POPhen, and both ligands hold a stronger extraction capacity for Th(IV) than U(VI) under the same experimental conditions. Both the slope analysis and spectroscopic studies indicated that POPhen extractants could form the sole 1:1 complexes with U(VI) and both 1:1 and 1:2 metal-to-ligand complexes with Th(IV). The structures of the 1:1 and 1:2 Th(IV) complexes with POPhen-type extractants were first elucidated by X-ray crystallography. This study will be helpful to deepen the understanding of the extraction effect and complexation mechanism of POPhen with high-valence actinide elements, providing a fundamental data basis and theoretical reference for the development of the advanced subsequent actinides separation process.