Hainan Island is the only large island located on the northern margin of the South China Sea and is surrounded by Cenozoic graben basins, including the Qiongdongnan, Yinggehai, and Beibuwan basins. The uplift and denudation history of the Jianfeng pluton on southwestern Hainan Island is significant for understanding the formation of the regional geomorphology and adjacent basin evolution. This paper presents apatite and zircon fission-track (FT) analyses conducted on the Jianfeng pluton. The zircon FT (ZFT) ages of the pluton range are from 63 ± 4 to 108 ± 8 Ma, and the apatite FT (AFT) ages are from 19.4 ± 1.8 to 43.9 ± 4.4 Ma. The average confined track lengths in apatite are relatively short (11.9–12.8 μm). An age–elevation plot indicates that two rapid cooling events occurred during 73–63 and 44–40 Ma. Thermal modeling revealed four stages of 73–63 Ma, 44–40 Ma, 40–11 Ma, and 11–0 Ma. From the Late Cretaceous to the middle Eocene (73–40 Ma), the Jianfeng area underwent episodic rapid uplift and denudation. At the end of the Late Cretaceous (73–63 Ma), the area was affected by mid-ocean ridge spreading in the Proto-South China Sea. During the middle Eocene (44–40 Ma), the Yinggehai Basin underwent abrupt expansion and subsidence, which increased the elevation difference between the Jianfeng area and the Yinggehai Basin. From the middle Eocene to the middle Miocene (40–11 Ma), the Jianfeng area underwent slow denudation, and the Yinggehai Basin was rapidly infilled, which eliminated the original elevation difference between the two areas. From the middle Miocene to the present (11–0 Ma), the Jianfeng area has undergone reactivated rapid uplift and denudation, which was driven by the remote effects of the India–Eurasia collision.