Improving the energy-saving efficiency of flue gas deep waste heat and reducing the emission of carbon dioxide and other pollutants have been two issues that need to be paid attention to in petrochemical heating furnaces. A hydrogen production reformer with high energy consumption and high carbon emissions in the petroleum refining process affects the thermal and productive efficiency of the hydrogen production, amounts of heat from flue gas are wasted with the exhausted corrosive gas of the reformer, and latent heat is not recovered. To recover the sensible and latent heat from the exhausted gas, a new anti-corrosion, high-efficiency, and low-pressure-drop flue gas condensing heat exchanger (FGCHE) with low consumption and pressure drop was developed. The energy-saving performance was evaluated through on-site measurements and theoretical analysis. The results show that the exhausted gas temperature was reduced from 161.3~175.9 °C to 33.9~38.9 °C after using the new FGCHE to recover waste heat. The energy-saving efficiency and the utilization ratio of flue gas waste heat were 12~16.1% and 74~81.9%, respectively. The latent heat accounted for 41.3~48.1% of the total recovered heat. The exergy efficiency and the total thermal efficiency of the reformer reached 73~86.8% and 95.2~96.6%, respectively. The condensation in the flue gas reduced pollutant emissions (SO2 and NOx). This paper provides a practical application reference for the technology development of waste heat recovery and the application of an FGCHE for petrochemical heating furnaces.