In this study, we describe for the first time the detonated ultrafast growth and functionalization of Iron (III) oxyhydroxide (FeOOH) nanorod array templates on a fluorine-doped tin oxide (FTO) substrate using a specially designed microwave-assisted cost-effective synthesis route. The rapid recrystallization and polycondensation in microwave-assisted synthesis (MAS) led to the controlled growth of ferric-hydroxide Fe(OH)3 from the iron-hydroxo complex Fe(H2O)3(OH)3 formed from hydrolyzed FeCl3. Further, the dependence of a number of MAS cycles on the growth and evolution of β-FeOOH nanorod array templated photoanode was examined by high-resolution scanning electron microscopy. The formation mechanism with morphology-controlled FeOOH nanostructure was well discussed and verified. Further, high-temperature quenching (HTQ) transformed MAS akaganeite into hematite, and Sn4+ diffused from FTO substrate. Due to the synergistic impact of MAS growth and Sn4+ diffusion in the α-Fe2O3 nanostructure, the optimum FTO/Fe2O3-1 photoanode achieved the highest photocurrent density (0.854 mA cm−2 at 1.23 V vs. RHE) related with other studied samples. The charge-transfer mechanisms in microwave-assisted Sn4+-diffused α-Fe2O3 nanostructure photoanodes are also investigated. Additionally, the surface-modified FTO/Fe2O3-1 photoanode exhibited the 91 and 180 μmol of oxygen and hydrogen evolution during photoelectrochemical water splitting, respectively. This work opens a sustainable and feasible strategy for designing and regulating high-efficient novel functional photoanode materials for water splitting.