In recent years, the depletion risk of fossil fuels has driven increasing interest in renewable energy. Among various technologies, proton exchange membrane fuel cells (PEMFCs) stand out due to their fast startup and high power density. However, the commonly used Nafion membranes suffer from reduced proton conductivity under low humidity and high temperatures, limiting their practical application. Polyoxometalates (POMs), with their excellent proton conductivity and thermal stability, have emerged as promising alternatives. Yet, their high water solubility raises safety concerns, and their water-dependent conduction mechanisms and structure–function relationships remain insufficiently understood. These issues hinder the practical development of POM-based proton conductors. This paper presents a comprehensive review of the key properties and proton conduction mechanisms of POMs, with a particular focus on POM crystals and their composites exhibiting high proton conductivity. Representative studies are analyzed to elucidate design strategies, structure–function relationships, and recent research progress over the past five years. Finally, perspectives and recommendations are proposed to inform future research directions and promote practical applications in the field of proton-conducting materials.