Thermal power plants will function as a flexible load regulation in a low-carbon grid, which requires operation adaption for the whole system. Energy transition in the electricity sector is the core to realizing carbon neutrality. The power grid will be gradually dominated by renewable energy, such as wind power and photovoltaic solar power. However, renewable energy has problems such as insufficient power supply and output fluctuation; thermal power will be required to regulate the peak load flexibly to meet demand. Therefore, the supply of boiler make-up water prepared by electrodeionization (EDI) in thermal power plants should also be flexibly changed. This study focused on the ultrapure water preparation system by EDI with variable flow rates. For an EDI system with a maximum ultrapure water capacity of 20 m3/h, the power consumption, annual cost, and carbon footprint of different designs are compared. The operation parameters were optimized based on the optimal cost design when the temporal demand of boiler make-up water is reduced to 75%, 50%, and 25%, respectively, considering thermal power as peak load regulation technology. The results showed that the optimized system could significantly reduce power consumption and carbon footprint by up to 30.21% and 30.30%, respectively. The proposed strategy is expected to be widely applied for design and operation optimization when considering the low-carbon but unstable energy system dominated by renewable energy. The carbon footprint could be a feasible optimization object to balance the greenhouse gas emissions from the module manufacturing and operation consumption.