Conjugated linoleic acid (CLA) has a variety of health‐promoting biological activities, and thus has a great potential as dietary supplement in functional foods. In our work, the effects of surface modifications of multiwalled carbon nanotubes (MWCNTs) support on the catalytic efficiency and selectivity of supported Ru catalysts for linoleic acid (LA) to CLA, as well as their influence mechanisms were well investigated. The results showed that the CLA yields for Ru/MWCNTs‐OH (36.45%) and Ru/MWCNTs‐COOH (31.06%) were significantly higher than that for Ru/MWCNTs (23.94%). This indicated that hydroxylated and carboxylated surface modification of MWCNTs could improve the catalytic activity of Ru. The CLA selectivity of Ru/MWCNTs‐N‐Doped and Ru/MWCNTs‐NH2 were up to 96.06% and 88.26%, respectively, and was also proved to be temperature and time dependent. TEM analysis indicated Ru nanoparticles were evenly attached on the surface of mMWCNTs but have little agglomeration on MWCNTs, and their particle sizes are negatively related to the catalytic efficiency. Further catalyst characterization by XPS demonstrated that high CLA selectivity of Ru/MWCNTs‐N‐Doped and Ru/MWCNTs‐NH2 were attributed to the high Ru (IV) content on the surface of supports. Thus, the mMWCNTs were proved to be the excellent support of Ru catalyst for high isomerization selectivity towards CLA formation.