AbstractRapidly and randomly drifted reference frames will shorten the transmission distance and decrease the secure key rate of realistic quantum key distribution (QKD) systems. In this article, we present a free-running reference-frame-independent (RFI) QKD scheme, where measurement events are classified into multiple slices with similar estimated classification parameter. We perform the free-running RFI QKD experiment with a fiber link of 100 km and reference frame misalignment more than 29 periods in 50.7 h. A key rate as high as 742.98 bps is achieved at the total loss of 31.5 dB benefiting from both the new protocol design and the 80 MHz repetition rate system in use. Our system runs 50.7 h freely without any reference frame alignment. In the experiment, the misalignment variation rate tolerance of the experiment is 0.262 rad/s, and could be optimized to 1.309 rad/s. Therefore, our free-running RFI scheme can be efficiently adapted into the satellite-to-ground and drone-based mobile communication scenarios.