Nanocrystalline BaCe0.7Zr0.1Y0.1Yb0.1O3−δ (BCZYYb) is designed by a novel strategy with improved proton transport properties at low temperatures (<300 °C). In situ Raman spectroscopy and electrical conductivity relaxation (ECR) are used to quantitatively evaluate the surface exchange coefficients during the hydrogen isotope exchange process. Similar surface exchange coefficients are measured via in situ Raman spectroscopy and ECR measurements, representing new tools to better understand proton transport behaviors at the materials’ interface. The surface exchange coefficient in nanocrystalline BCZYYb is nearly four times higher than that in conventional dense BCZYYb at 300 °C, indicating higher surface mobility of protonic species in the designed BCZYYb membrane. The improved performance originates from the combined interfacial and bulk effects for proton transport at low temperatures. In addition, low‐temperature protonic ceramic fuel cells (PCFCs) are built based on a nanocrystalline BCZYYb electrolyte with improved single‐cell performance at 300 °C, which indicates enhanced proton transport properties in contemporary energy conversion and storage materials can be achieved through interfacial engineering.