The heat generated by a proton exchange membrane fuel cell (PEMFC) is generally removed from the cell by a cooling system. Combining heat energy and electricity in a PEMFC is highly desirable to achieve higher fuel efficiency. This paper describes the design of a new power system that combines the heat energy and electricity in a miniature PEMFC to improve the overall power efficiency in an underwater glider. The system makes use of the available heat energy for navigational power of the underwater glider while the electricity generated by the miniature PEMFC is used for the glider's sensors and control system. Experimental results show that the performance of the thermal engine can be obviously improved due to the high quality heat from the PEMFC compared with the ocean environmental thermal energy. Moreover, the overall fuel efficiency can be increased from 17 to 25% at different electric power levels by harvesting the PEMFC heat energy for an integrated fuel cell and thermal engine system in the underwater glider.