The influence of cobalt crystallite size on catalyst performance in Fischer–Tropsch synthesis (FTS) has been investigated using functionalized carbon nanotube (CNT)-supported catalyst. The catalysts were synthesized by the core reverse micelle reactions with cobalt crystallites of various sizes. It has been shown that crystallite size is dependent to the water-to-surfactant ratio (3–10) used for the catalyst preparation. The catalysts were characterized by Brunauer–Emmett–Teller method (BET), X-ray diffraction (XRD), H 2 chemisorption, temperature program reduction (TPR), and transmission electron microscopy (TEM). According to TEM analysis, small cobalt crystallites size (3–8nm) synthesized by microemulsion technique have a very narrow size distributions, and they were mostly confined inside the functionalized CNT. The deposition of cobalt nanoclusters synthesized by microemulsion technique on the functionalized CNT, shift the reduction peaks to a low temperature, indicating higher reducibility for uniform cobalt crystallites. The catalyst prepared with functionalized CNT using proposed microemulsion technique, increased the FTS rate from 0.64 to 0.78g HC/g cat./h, C 5 + selectivity increased 7.4% and CH 4 selectivity decreased 44%, compared to that catalyst prepared on common CNT.