Flow of partially molten crust is a key contributor to mass and heat redistribution within orogenic systems, however, this process has not yet been fully understood in accretionary orogens. This issue is addressed in a Devonian migmatite-granite complex from the Chinese Altai through structural, petrological, and geochronological investigations presented in this study. The migmatite-granite complex records a gradual evolution from metatexite, diatexite to granite and preserves a record of two main Devonian phases of deformation designated D1 and D2. The D1 phase was subdivided into an early crustal thickening episode (D1B) and a later extensional episode (D1M) followed by D2 upright folding. The D1M episode is associated with anatexis in the deep crust. Vertical shortening, associated with D1M, gave rise to the segregation of melt and formation of a sub-horizontal layering of stromatic metatexite. This fabric was reworked by the D2 deformation associated with the migration of anatectic magma in the cores of F2 antiforms. Geochronological investigations combined with petro-structural analysis reveal that: (1) D1M partial melting started probably at 420−410 Ma and formed sub-horizontal stromatic metatexites at ∼30 km depth; (2) The anatectic magma accumulated and migrated when a drainage network developed, as attested by the pervasive formation of massive diatexite migmatites, at 410−400 Ma; (3) Soon after, massive flow of the partially molten crust from orogenic lower to orogenic upper crustal levels, assisted by the interplay between D2 upright folding and magma diapirism, led to migmatite-granite emplacement in the cores of regional F2 antiforms that lasted until at least 390 Ma; (4) a terminal stage was manifested by the emplacement of 370−360 Ma granite dykes into the surrounding metamorphic envelope. We propose that Devonian anatexis assisted by deformation governed first the horizontal and then the vertical flow of partially molten orogenic lower crust, which drove crustal flow, mass redistribution, and crustal differentiation in the accretionary system of the Chinese Altai.