Gega lake, in southeastern Tibet, was formed by the blocking of Yarlung Tsangpo gorge by a glacier and is a well-known example of geomorphological damming. However, the evolution of the damming process at the site is still not understood in detail. Here, we use measurements of multiple magnetic parameters of the sediments from the Yusong (YS) 3 section, which is well-dated by optically stimulated luminescence, to provide a detailed history of the late stage of Gega dammed lake since 17.0 ka. Low-frequency field magnetic susceptibility (χlf) increases upwards gradually from 25 to 79 × 10−8 m3/kg above 5.5 m, but other magnetic properties, such as frequency-dependent magnetic susceptibility (χfd % and χfd), susceptibility of anhysteretic remanent magnetization (χARM), and saturation isothermal remanent magnetization (SIRM) did not show a similar degree of enhancement. The magnetic grain size indicators of χARM/χlf, χARM/SIRM, and χlf/SIRM all indicate a trend of increasing magnetic grain size from the 5.5 m to the top of section; however, the bulk sediment grain size decreases gradually within the same interval. The total organic carbon is very low (0.2–0.7%), and thus, it is unlikely that the sedimentary environment is sufficiently strongly reducing to lead to the dissolution of magnetic minerals. Therefore, we infer that the coarsening-upwards of the magnetic grain size, and the increasing magnetic susceptibility from 5.5 m, reflect the gradual preferential preservation of magnetic minerals, caused by the deepening of the lake. Thus, we interpret the magnetic record of the section as reflecting the gradual deepening of the late stage of Gega ice-dammed lake. Last, the abrupt disappearance of the lake may have resulted in an outburst flood.