Multi-guest clathrates exhibit lots of functional characteristics owing to their unique structures, which herald beautiful application prospects, but their fundamental information is still scarce. Herein, we explore a type of (helium, excess electrons/EEs)–C60F60 co-clathrates with quasi-Matryoshka-doll structures using ab initio molecular dynamics simulation and reveal the EEs-entangled He roaming dynamics in C60F60 and its effect on the characteristics of clathrates. Perfluorination ensures that C60F60 possesses an extremely electropositive interior cavity. Its unique confinement effect can stabilize He as an extremely inert entity by noticeably enlarging the 1s–2s orbital gap and can also trap 1–2 EEs in its s-type interior orbital with extremely large binding energies. Co-inclusion of He and EEs in C60F60 exhibits inter-repulsive He⋯EEs entangling dynamics featuring quasi-Matryoshka-doll structures (He@EEs@C60F60). In this structure, EEs screen the attraction of cage-shell Cδ+ to He 1s2 electrons, thus inhibiting their stabilization and orbital expansion, while He conversely decreases the stability of EEs and redshifts their transition absorption. He can roam in the cavity, but its trajectory is impacted by EEs serving as a medium, and thus, the structures exhibit anormal dynamic variation of internuclear He⋯C spin coupling JHeC, which is manipulated by the EEs-entangled He roaming dynamics. JHeC and JHeC′ present opposite distance dependences for the colinearly aligned C⋅⋅⋅He⋅⋅⊗⋅⋅⋅⋅⋅C′ (⊗, the cage center). This work provides insights into the Matryoshka-doll structured He@EEs@C60F60 with He–EEs entangling dynamics and its modulation on EEs absorption and reveals the dynamic role of EEs in manipulating He-roaming and JHeC coupling properties for promising applications.