Amphibole is an important mineral during the differentiation of arc magmas but rarely as a phenocryst in arc lavas or eruptive pyroclastic rocks. The Sanggeda complex, intruded into the ophiolite of the Indus–Yarlung Zangbo Suture Zone (IYZSZ), Zedong, southern Tibet, mainly consists of amphibole-rich, fine-grained, and porphyritic gabbros. The complex provides an opportunity to study the differentiation of arc magmas through amphibole crystals. Four distinct amphibole crystal populations can be recognized according to petrographic observations, EMPA, and LA–ICP–MS analysis. The first ones (Type 1) are fined-grained and euhedral, are crystallized during ascent, and are the product of the shallow emplacement of host magma. The second ones (Type 2) are euhedral, with slight negative Eu and Sr anomalies, and crystallize from an evolved magma that previously experienced plagioclase fractionation. Type 3 amphiboles have similar morphological characteristics to Type 2 but are without Eu and Sr anomalies. Type 4 crystals are shown as pseudomorphs, formed by the reaction–replacement between the clinopyroxene and melt. Type 1 crystals are autocrysts. Other amphiboles within host magma, whether presented as phenocrysts or cumulate nodules, are antecrysts. Based on the amphibole crystal population developed in the complex, in this study, a trans-crustal magma plumbing system is proposed, containing at least three magma reservoirs located at different crust depths: the shallow emplaced crust (~4.8 km), the mid-crust (~12.9 km), and the lower crust (~21.8–24.9 km). Early amphibole crystallization is an effective process to generate silicic residual melts. Gravity could help in that sense. Precursor amphibole and clinopyroxene can efficiently delaminate back into the mantle and promote the generation of silicic continental crust.