Abstract By using the combination of concentrated nitric acid refluxing, varied thermal treatment and wetness impregnation method on carbon nanotubes (CNTs), we realized the controllable encapsulation of cobalt clusters inside the channels of CNTs. The analysis results by TPD and TEM on the prepared cartalysts indicated that the controllable encapsulation of cobalt clusters in CNTs channels was realized more readily by controlling the thermal treatment on pristine CNTs support at different temperature. For the Co/CNTs-650 catalyst employing thermal treated CNTs at 650°C, the cobalt nanoparticles inside the CNTs channel reached up to 80% with the particles size of 5–10nm. The thermal treatment on the pristine CNTs support at this optimized temperature effectively removed the oxygen-containing functional groups on the surface of CNTs, simultaneously keeping the integrity of CNTs walls. The influence of varied thermal treatment of the CNTs support to the catalytic performance of the final Co/CNTs catalysts in the Fischer–Tropsch synthesis (FTS) was investigated. The FTS reaction results on the Co/CNTs-650 catalyst showed both the best CO conversion of 89.3% and the highest C5+ hydrocarbon selectivity of 83.7%, at the same time holding the lowest CH4 selectivity of only 8.4% among all the tested FTS catalysts.