Judicious interfacial-, crystalline- and structural-engineering of plasmonic metal-semiconductor nanocomposites is key to harnessing their plasmonic functions for enhancing solar energy conversion. In this work, metal@semiconductor core-shell nanocrystals with atomically organized interface, quasi-monocrystalline shell and diverse controllable structures/morphologies, which are hardly tractable by conventional synthetic strategies, are accessed by developing an aqueous cation exchange method. The combined studies including Mid-IR femtosecond transient absorption spectroscopy measurements show that the superior metal-semiconductor interface attained by the presented method can greatly promote the extraction of hot electrons from metal to semiconductor (the quantum yield of hot electron injection was estimated at ~ 48%) in comparison with the nanostructures bearing unoptimized interfaces. Thus produced metal@semiconductor nanocrystals give 2–3 orders of magnitude enhancement in photocatalytic H2 evolution activity relative to their counterparts accessed by conventional methods.