In the process of using thin-film thermocouples for contact measurement of the reaction temperature in proton exchange membrane fuel cells (PEMFC), the impact of thin-film thermocouple volume on the system’s reaction temperature field variation, reaction efficiency, and the lifespan of thermocouples under these conditions is not thoroughly studied. Using magnetron sputtering technology, NiCr/NiSi thin-film thermocouples (NiCr/NiSi TFTCs) with different junction sizes were fabricated on the proton exchange membrane (PEM). These NiCr/NiSi TFTCs exhibit excellent compactness, with thickness and planar dimensions in the micrometer range. When PEMFCs are equipped with built-in NiCr/NiSi TFTCs of different hot junction sizes, the time required for the system to reach a steady state varies with the size of the hot junction, with smaller hot junction sizes reaching a steady state more quickly. In a 500-h continuous operation test, the failure rates of NiCr/NiSi TFTCs also vary based on the hot junction size. Both smaller and larger hot junction sizes have relatively higher failure rates, whereas medium-sized junctions have a lower failure rate. These extensive and repetitive comparative experiments provide significant reference value for the size design of TFTCs operating inside PEMFCs, promoting both industrial production and scientific research.