In response to the issue of the hydropower consumption of run-of-river hydropower stations in Southwest China, the district cooling system can provide regulation capacity for hydropower utilization and suppress fluctuations caused by the uncertainty of hydropower. The innovative method is to utilize the thermal characteristics of pipelines and buildings, as well as the thermal comfort elasticity to shift the cooling and electricity loads, which helps to consume the surplus hydroelectric power generation. Taking the minimum total cost of coal consumption in thermal power units, hydropower abandonment penalty, and the carbon trading cost as the objective function, models were established for power supply balance constraints, heat transport constraints, and unit output constraints. The hybrid integer linear programming algorithm was used to achieve the low-carbon economic dispatch of the electric-cooling system. The calculation examples indicate that compared to the traditional real-time balance of cooling supply, the comprehensive consideration of thermal characteristics in a cooling system and flexible thermal comfort have a better operational performance. The carbon trading cost, coal consumption cost, and abandoned hydropower rate of a typical day was reduced by 4.25% (approximately CNY 7.55 × 104), 4.47% (approximately CNY 22.23 × 104), and 3.66%, respectively. Therefore, the electric-cooling dispatch model considering the thermal characteristics in cooling networks, building thermal inertia, and thermal comfort elasticity is more conducive to the hydropower utilization of run-of-river stations.