Magnesium (Mg) stable isotope ratios reflect Mg turnover in ecosystems. At the Hailuogou glacial retreat chronosequence in SW China, about one-third of the initially present Mg was lost from the topsoil in 127 years. We determined bulk soil and exchangeable δ26Mg values at six sites exposed by the glacier from 0 to 127 years ago. Moreover, we conducted a weathering experiment (pHstat) at the youngest (0 years) and the oldest (127 years) sites and measured δ26Mg values in differently reactive pools. We found a close correlation between the δ26Mg values of the bulk topsoils (0–10 cm) and the Mg depletion rates (r = 0.98, p < 0.001, n = 5). The particularly fast Mg loss in the first 37 years was attributable to leaching of exchangeable Mg and the fast dissolution of chlorite as revealed by the lower δ26Mg values of the fast- (−1.28 ± 0.10‰) than the slow-reacting (−0.64 ± 0.11‰) pool at the 0 year-old site in our pHstat experiment. The low δ26Mg values of the fast-reacting pool matched those reported for chlorite. Our results indicate that the δ26Mg values might be used as proxy of Mg loss and to identify the mineral sources of this loss.