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Here we reported a novel technology using parylene-cross-linking structure to achieve on-chip air-gap thermal isolation for microfluidic system-on-chip (SOC) applications. Two applications based on this technology, on-chip continuous-flow polymerase chain reaction (PCR) and on-chip temperature gradient liquid chromatography (LC) were successfully demonstrated. Device thermal performance in each example was characterized. Results showed that our technology not only provides excellent on-chip thermal isolation but also its simplicity of integration with other on-chip components makes versatile microfluidic SOC applications feasible.