Methanol is considered as a promising hydrogen carrier in accelerating the carbon-neutral applications of fuel cell cogeneration. However, the methanol reforming process emits CO2 whose efficient recycling is challenging due to the inevitable power and cooling consumption. To this end, this paper considers the methanol reforming based high-temperature proton exchange membrane fuel cells (HT-PEMFC) cogeneration system, equipped with ammonia absorption power-refrigeration cycle (APRC). The waste heat in the integrated system is utilized for the fuel preheating, evaporation and reforming, driving APRC, and water heating, achieving a cascaded utilization of thermal energy. By building the mathematical models for each subsystem, thermodynamic and economic assessments are investigated. The results confirm that the waste heat of HT-PEMFC is sufficient to drive both methanol reforming and APRC, with additional electricity output from APRC. At a current density of 0.53 A/cm2, the exergy efficiency of the integrated system under the design condition is 0.525 and reaches a maximum value of 0.565 at a reaction temperature of 180 °C and pressure of 1.2 bar. The techno-economic analysis reveals a dynamic payback period of 5.2 years and net present value of 1.14 M$ with a 20-year lifespan of the integrated system.