Exploring high-performance zeolite-supported metal catalysts is of great significance. Herein, we develop a strategy for fabricating isolated single metal atomic site catalysts in Y zeolite (M-ISAS@Y, M = Pt, Pd, Ru, Rh, Co, Ni, Cu) by in situ separating and confining a metal–ethanediamine complex into β-cages during the crystallization process followed by thermal treatment. The M-ISAS are stabilized by skeletal oxygens of Y zeolite, and the crystallinity, porosity, and large surface area are well inherited in M-ISAS@Y. As a demonstration, acidic Pt-ISAS@Y is used for n-hexane isomerization involving consecutive catalytic dehydrogenation/hydrogenation on Pt-ISAS and isomerization on Brønsted acid sites. The turnover frequency value of Pt-ISAS reaches 727 h–1, 5 times more than Pt nanoparticles (∼3.5 nm), with a total isomer selectivity of more than 98%. This strategy provides a convenient route to fabricate promising zeolite-based M-ISAS catalysts for industrial applications.