Manipulating physical properties through ion migration in complex oxide thin films is an emerging research direction to achieve tunable materials for advanced applications. While the reduction of complex oxides has been widely reported, few reports exist on the modulation of physical properties through a direct hydrogenation process. Here, we report an unusual mechanism for hydrogen-induced topotactic phase transitions in perovskite La0.7Sr0.3CoO3 thin films. Hydrogenation is performed upon annealing in a pure hydrogen gas environment, offering a direct understanding of the role that hydrogen plays at the atomic scale in these transitions. Topotactic phase transformations from the perovskite (P) to hydrogenated-brownmillerite (H-BM) phase can be induced at temperatures as low as 220 °C, while at higher hydrogenation temperatures (320-400 °C), the progression toward more reduced phases is hindered. Density functional theory calculations suggest that hydroxyl bonds are formed with the introduction of hydrogen ions, which lower the formation energy of oxygen vacancies of the neighboring oxygen, enabling the transition from the P to H-BM phase at low temperatures. Furthermore, the impact on the magnetic and electronic properties of the hydrogenation temperature is investigated. Our research provides a potential pathway for utilizing hydrogen as a basis for low-temperature modulation of complex oxide thin films, with potential applications in neuromorphic computing.