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As one of the microcontinents dispersed in the South China Sea (SCS), the Xisha microcontinent lacks the petrological evidence of the Cenozoic magmatic activity and basement. Well CK‐2, as a full‐coring kilometre‐scale major scientific drilling in Xisha Islands in the northwestern SCS, drilled through the thick reefal limestone and into the underlying basaltic pyroclastic rocks basement. This paper presents zircon U–Pb age and mineral chemistry of clinopyroxenes from the basaltic pyroclastic rocks. Mineral composition of the clinopyroxenes suggests that most of the clinopyroxenes are composed of diopside, which contains relatively high Al(w (Al2O3) = 5.03%–10.25%) and Ti(w (TiO2) = 2.2%–4.95%). The clinopyroxene discrimination diagrams show that the primary magma is alkaline basalt and likely generated in an intraplate tectonic setting. U–Pb dating of zircons by LA‐ICP‐MS yielded a wide range of ages: 36–33, 116–104, 148–140, 207–196, 255–236, 440, 808–749, and 2,440–1185 Ma. The youngest group has an average age of 35.5 ± 0.9 Ma, which is considered as the maximum age of the basalt eruption. The 2440 ± 19 Ma, which is the oldest zircons in the SCS, are firstly found in the basaltic pyroclastic rocks from the SCS, suggesting that the SCS may contain very old materials. The ages of the inherited zircons are comparable to magmatic activities that occurred around the SCS, implying that they were probably once linked and an integrated part of Gondwana. The ancient continental basement has experienced multistages magmatic events. [ABSTRACT FROM AUTHOR]