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We report here a new strategy for the control of hydrocarbon selectivity in Fischer–Tropsch (FT) synthesis using silica yolk–shell ruthenium nanoreactors prepared in water/oil (W/O) microemulsions. The sizes of nanoreactors have been varied by changing the microemulsion composition. Nanoreactors prepared with the smallest internal volume exhibited a restriction of hydrocarbon chain length growth during FT synthesis. An increase in the nanoreactor volume resulted in a gradual shift of the hydrocarbon distribution to longer-chain hydrocarbons till a distribution of hydrocarbons reached that observed over the reference catalysts prepared by deposition of non-encapsulated metal nanoparticles on silica supports. The observed remarkable modifications of hydrocarbon selectivity over Ru nanoreactors have been explained by shape selectivity effects on hydrocarbon growth due to decrease in entropy in comparison with infinite growth and increase in the Gibbs energy for growing hydrocarbon chains located inside the limited volumes of nanoreactors.