Volcaniclastic rocks are important unconventional oil and gas reservoirs from which it is difficult to determine the protolith due to strong metasomatic alteration. Intensive alteration has occurred in much of western China, but few robustly documented examples are known from which to assess the alteration processes. Further recognition from the petrological and mineralogical record is essential to quantify the diagenetic environment, the degree of alteration, and its impacts. Permian volcanic rocks are widely developed in the western Sichuan Basin (southwestern China), with a thickness of more than 200 m. The thickness of volcaniclastic rocks in the Permian Emeishan Basalt Formation is up to 140 m, with a 5600~6000 m burial depth. In this study, we demonstrate an approach to recognizing hydrothermal alteration by the occurrence of scapolite megacryst mineral pseudomorphs (SMMPs) in Permian volcaniclastic rocks in the Sichuan Basin (southwestern China). The results show that SMMPs in the Permian volcaniclastic rocks in the western Sichuan Basin mainly occur in the lower part of the Permian basalts as intragranular minerals and rock inclusions. Scapolite is transformed into quartz and albite, and only the pseudomorph is preserved, indicating secondary hydrothermal fluid metasomatic alteration. Scapolite is formed after microcrystalline titanite and is the product of the high-temperature pneumatolytic metasomatism of plagioclase from the mafic protolith during the post-magmatic stage. The mixing of meteoric water and barium-rich hydrothermal fluid leads to the precipitation of barite; additionally, the pores are filled with barite and halite after the alteration of scapolite. The silicification and hydrothermal dissolution of scapolite and the albitization of sodium-rich matrix minerals increase the pore volume, which is conducive to the later recharge by hydrothermal fluids. The discovery of SMMPs can serve as an indicator of the high-temperature pneumatolytic metasomatism and mixing of meteoric water and deep hydrothermal fluid.