We propose and demonstrate a photon-counting optical time-domain reflectometry using a free-running Single-Photon Avalanche Detector (SPAD). A negative feedback InGaAs/InP single-photon avalanche diode, which can quickly quench the avalanche current and suppress the after pulsing effect is the core component of the homemade SPAD. The homemade SPAD operates in free-running mode, with a maximum detection efficiency of 35% at a wavelength of 1550 nm and a time jitter of 80 ps. We experimentally demonstrated that the photon-counting optical time-domain reflectometry based on a homemade free-running SPAD can achieve fast measurement. The measurement time is ~10 s, the distance is ~90 km, and the dynamic range is ~20 dB. Furthermore, we achieved a two-point resolution of ⪅ 5 m at the end of a 90 km distance.