Focusing on waste heat recovery from the flue gas of a 5.6 MW gas-fired boiler in a heating plant in Beijing, this study designs two deep flue gas heat recovery schemes—direct heat exchange and electric vapor-compression heat pump—leveraging the low-temperature return water conditions of the secondary heating network. Based on measured operational parameters, a hybrid operation mode incorporating peak–valley electricity pricing is proposed, and a techno-economic evaluation is conducted on three operation modes. The results indicate that the direct recovery mode offers a simpler system configuration and higher system energy efficiency ratio, yet results in relatively higher exhaust gas temperatures. In contrast, the heat pump recovery mode requires three or more compressors to achieve greater heat exchange capacity and lower exhaust temperatures. Under the direct recovery mode, the first heat exchanger bears the majority of the temperature drop, and a single unit suffices under low-load conditions. The direct recovery mode demonstrates the best economic performance, with a payback period of only 1.47 years. The hybrid operation mode balances initial investment and operational revenue, shortening the payback period of the heat pump-involved system from 11.82 years to 4.59 years. The system can reduce carbon emissions by 29.18 tCO? to 65.01 tCO? annually.