The synergistic integration of optofluidic and surface enhanced Raman scattering (SERS) sensing is a new analytical technique that provides a number of unique characteristics for enhancing the sensing performance and simplifying the design of microsystems. Here, we propose a reusable optofluidic SERS sensor by integrating Au nanoisland substrate (AuNIS)-coated fiber into a microfluidic chip. Through both systematic experimental and theoretical analysis, the sensor enables efficient self-cleaning based on its optical-to-heat-hydrodynamic energy conversion property. Besides, the sensor exhibits the instrument detection limit down to 10-13mol/L and enhancement factor of 106 for Rhodamine 6G. Our optofluidic SERS sensor with such a photothermal microfluidic-assisted self-cleaning method has the advantages of portability, simple operation, and high cleaning efficiency, which will provide a new, to the best of our knowledge, concept and approach for cost-effective and reusable sensors.