Koktokay No. 3 pegmatite is a globally renowned rare metal deposit. Recently, rare metal-enriched leucogranite was identified within this deposit. The leucogranite is locally cut by No. 3 pegmatite and scattered as fragments among the pegmatite in some outcrops. In this study, we aimed to investigate the emplacement depth, thermal history, and evolution process of leucogranite based on quartz chemical composition and apatite thermochronology. Li, Al, P, Ge are the higher content elements in leucogranite quartz, and Ti is the lower content element (approximately 38.7, 178, 23.9, 2.7, and 2.0 ppm, respectively). The Al, Ti, and Li contents decreased from the core to the rim of the quartz. The leucogranite quartz compositions have a high Ge/Ti ratio, similar to that of the quartz in the Li-Cs-Ta pegmatites, particularly the Koktokay No. 3 pegmatite. This similarity indicates that the leucogranite was formed by a highly evolved melt. Using laser ablation-inductively coupled plasma-mass spectrometry, the U–Pb age of leucogranite apatite was determined as 189.4 ± 6.8 Ma, which is substantially younger than the previous columbite U–Pb age of No. 3 pegmatite, suggesting that the magmatic-thermal activity of No. 3 pegmatite had interfered with the apatite U–Pb closure system. The apatite low-temperature thermochronology results showed that the thermal history of leucogranite can be divided into two cooling stages: rapid cooling stage (180–155 Ma, 9.6–10.6 ℃/m.y.) and slow cooling stage (from 155 Ma to the present day, 0.8–1.0 ℃/m.y.). According to the thermal history, the exhumation and erosion of the Koktokay No. 3 rare-metal deposit is at least 5–6 km long. Leucogranite formation pressure is approximately 2.5 kbar (1.8–3.7 kbar), and the emplacement depth approximately 9.5 km (7–14 km).