The generation of a long-lived charge-separated state in versatile π-conjugated two-dimensional covalent organic frameworks (2D COFs), a process essential to extending their great potentials in advanced semiconducting applications, is yet fully elucidated. Herein, we report a systematic investigation of the photophysical properties of three highly crystalline imine-linked 2D COFs using steady-state and transient absorption spectroscopy accompanied by time-dependent density functional theory (TDDFT) calculations. The different electron affinity between 5,5',5″-(1,3,5-benzenetriyl)tris(2-pyridinecarboxaldehyde) (BTPA) and three tunable electron-donating/accepting triamine monomers dominated the formation of the excited-state, charge-transfer direction, and lifetime. A prominent charge transfer from electron-rich 4,4',4″-triaminotriphenylamine (TAPA) to BTPA in COFTAPA-BTPA led to the long-lived charge-separated state, which was attributed to a greater degree of delocalization compared to the two other COFs. These results provide fundamental insight into the importance of structure-property correlation for designing advanced photoactive 2D COF materials with the efficient charge transfer and long-lived charge-separated state.