Low-oxygen (O₂) environments are essential in various research and application fields, yet traditional methods like nitrogen flushing or chemical O₂ absorbers face challenges in high equipment cost and low controllability. This study introduces a novel electrochemical oxygen removal (EOR) controller, offering a lightweight, low-cost, and precise low-O₂ control solution. The self-powered EOR controller uses a sacrificial anode to drive the cathodic oxygen reduction reaction (ORR), efficiently consuming environmental O₂ to reduce its level, thus eliminating the requirements of external gas or power sources. By integrating a single-atom ORR catalyst and flexible design, the device achieves a substantial reduction in weight and cost. The incorporation of electronic components for the EOR controller, including a switch for reaching targeted O₂ concentration and a fixed resistor for O₂ removal rate regulation, enables multi-dimensional O₂ removal control. The system also realizes the O₂ concentration estimation in real-time with ±1% accuracy (within the 21%–1% range) by calculating electron transfers. The EOR controller’s effectiveness is validated in plant hypoxia stress experiments, demonstrating precise O₂ level adjustments and its potential across various applications requiring controlled hypoxic conditions.