We propose and demonstrate a highly sensitive in-line photonic crystal fiber (PCF) microfluidic refractometer. Ultrathin C-shaped fibers are spliced in-between the PCF and standard single-mode fibers. The C-shaped fibers provide openings for liquid to flow in and out of the PCF. Based on a Sagnac interferometer, the refractive index (RI) response of the device is investigated theoretically and experimentally. A high sensitivity of 6621 nm/RIU for liquid RI from 1.330 to 1.333 is achieved in the experiment, which agrees well with the theoretical analysis.