Shortly after the cessation of seafloor spreading, intraplate magmatism affected large areas in the South China Sea (SCS) region. The origin and geodynamic setting of the post-spreading volcanism is still in debate, for many previous studies have focused on petrogenesis and mantle source of the late Cenozoic basalts from the SCS region. In this study, we obtained in situ major element compositions (by using Electron microprobe analysis—EMPA) and trace element compositions (by using laser ablation inductively coupled plasma mass spectrometry— LA-ICP-MS) for minerals (clinopyroxenes (Cpx), plagioclases (Pl), and olivines (Ol)) hosted by late Cenozoic basaltic rocks from Thailand. The results showed that the olivines had forsterite contents between 60.12% and 84.74%. Clinopyroxene were diopside and augite, and they were enriched in light rare earth elements (LREEs) (LaN/YbN = 1.93–4.27) and depleted in large-ion lithophile elements (LILEs). Mineral compositions (mainly based on clinopyroxene) confirmed that these late Cenozoic basaltic rocks were of an intraplate affinity and were similar to contemporaneous basaltic fields in the SCS region (Southern Vietnam, Northern Hainan, and SCS seamounts). Plagioclases were predominantly labradorite, with a few andesine and bytownite, and they were enriched in LREEs and Ba, Sr, and Pb, and most of them exhibited strong positive Eu anomalies. The source lithology of Thailand basaltic rocks could be garnet pyroxenite. The mantle potential temperature beneath Thailand is in the range of 1448–1467 °C, which can be comparable to those beneath Southern Vietnam and Northern Hainan, indicating the Thailand basaltic rocks could be produced by the Hainan mantle plume. In addition, the crystallization temperature of clinopyroxenes (1145–1214 °C) and plagioclase (1067–1133 °C) and their composition characteristics indicate that the magmatic processes have a conspicuous characteristic of fast rate of magma upwelling. Thus, we proposed that the deep geodynamic setting of Thailand late Cenozoic basaltic rocks is similar to those of the whole SCS region, and Hainan mantle plume plays a significant role in the petrogenesis of these basaltic rocks.