Herein, a spiro rhodamine (Rho)-thionated naphthalimide (NIS) electron donor-acceptor orthogonal dyad (Rho-NIS) was prepared to study the formation of a long-lived charge separation (CS) state via the electron spin control approach. The transient absorption (TA) spectra of Rho-NIS indicated that the intersystem crossing (ISC) occurs within 7-42 ps to produce the 3NIS state via the spin orbit coupling ISC (SOC-ISC). The energy order of 3CS (2.01 eV in n-hexane, HEX) and 3LE states (1.68 eV in HEX) depended on the solvent polarity. The 3NIS state having n-π* character and a lifetime of 0.38 μs was observed for Rho-NIS in toluene (TOL). Alternatively, in acetonitrile (ACN), the long-lived 3CS state (0.21 μs) with a high CS state quantum yield (ΦCS, 97%) was produced with the 3NIS state as the precursor and the CS took 134 ps. On the contrary, in the case of the reference Rho-naphthalimide (NI) Rho-NI dyad without thionation of its carbonyl group, a long-lived CS state (0.94 μs) with a high energy level (ECS = 2.12 eV) was generated even in HEX with a lower ΦCS (49%). In the presence of an acid, the Rho unit in the Rho-NIS adopted an open form (Rho-o) and the 3NIS state was produced within 24-47 ps with the 1Rho-o state as the precursor. Subsequently, slow intramolecular triplet-triplet energy transfer (TTET, 0.11-0.60 μs) produced the 3Rho-o state (9.4-13.6 μs). According to the time-resolved electron paramagnetic resonance (TREPR) spectra of NIS-NH2, the zero-field splitting (ZFS) parameter |D| and E of the triplet state were determined to be 6165 MHz and -1233 MHz, respectively, indicating that its triplet state has significant nπ* character, which was supported by its short triplet state lifetime (6.1 μs).