In this paper, the authors studied the major elements,trace elements, ⁸⁷Sr/⁸⁶Sr isotopes and water content of clinopyroxene megacrystals hosted by Maguan alkali basalt in southeastern Yunnan Province. All clinopyroxene megacrystals are aluminum augite, and their Mg^# are negatively correlated with Al, Fe, Ti, but positively correlated with Ca. MREE is relatively more enriched than HREE and LREE. The LILE (large ion lithophile elements) are obviously deficient. The HFSE (high field strength elements) Nb and Zr are depleted, but Hf is slightly enriched. Nb, Ta and Zr, Hf fractionation is obvious respectively, and Rb and Zr change dramatically. The ⁸⁷Sr/⁸⁶Sr ratios range from 0.703 92 to 0.705 06. All these data suggest that the clinopyroxene megacryst originated from the same parent magma as the hosted alkali basalt. The water content of clinopyroxene megacrystals is 318×10^-6~693×10^-6as measured by Micro-FTIR, which is richer than that of Nushan and Hanoba as well as the peridotite xenolith in Maguan. It indicates that the upper mantle is rich in water in the study area, suggesting oceanic subduction in Cenozoic. The western Pacific Ocean crust which reached the transitional zone retreated eastward in Neogene, whereas the Neo-Tethys ocean crust subducted northeastward. These factors were probably responsible for the abundant water in Maguan mantle. Subsequently, mgama was formed in the asthenosphere (or mantle transition zone) by the Neo-Tethys ocean crust subduction.