We report here our systematic characterization of a photoinduced electron-transfer (ET) redox cycle in a covalently linked donor-spacer-acceptor flexible system, consisting of N-acetyl-tryptophan methylester as electron donor and thymine as electron acceptor in three distinct solvents of water, acetonitrile and dioxane. With femtosecond resolution, we determined all the ET time scales, forward and backward, by following the complete reaction evolution from reactants, to intermediates and finally to products. Surprisingly, we observed two distinct ET dynamics in water, corresponding to a stacked configuration with ultrafast ET in 0.7 ps and back ET in 4.5 ps and a partially folded C-clamp conformation with ET in 322 ps but back ET in 17 ps. In acetonitrile and dioxane, only the C-clamp conformations were observed with ET in 470 and 1068 ps and back ET in 110 and 94 ps, respectively. These relatively slow ET dynamics in hundreds of picoseconds all showed significant conformation heterogeneity and followed a stretched decay behavior. With both forward and back ET rates determined, we derived solvent reorganization energies and coupling constants. Significantly, we found that solvent molecules intercalated in the cleft of the C-clamp structure mediate electron transfer with a tunneling parameter (β) of 1.0–1.4 Å−1 and the high-frequency vibration modes in the product(s) couple with the back ET process, leading to the ultrafast back ET dynamics in tens of picoseconds. These findings provide mechanistic insights of nonequilibrium ET dynamics modulated by conformation flexibility, mediated by unique solvent configuration, and accelerated by vibrational coupling.