This review emphasizes the importance of the catalytic conversion techniques in the production of clean liquid and hydrogen fuels (XTF) and chemicals (XTC) from the carbonaceous materials including coal, natural gas, biomass, organic wastes, biogas and CO2. Dependence of the performance of Fischer–Tropsch Synthesis (FTS), a key reaction of the XTF/XTC process, on catalyst structure (crystal and size) is comparatively examined and reviewed. The contribution illustrates the very complicated crystal structure effect, which indicates that not only the particle type, but also the particle shape, facets and orientation that have been evidenced recently, strongly influence the catalyst performance. In addition, the particle size effects over iron, cobalt and ruthenium catalysts were carefully compared and analyzed. For all Fe, Co and Ru catalysts, the metal turnover frequency (TOF) for CO hydrogenation increased with increasing metal particle size in the small size region i.e., less than the size threshold 7–8 nm, but was found to be independent of particle size for the catalysts with large particle sizes greater than the size threshold. There are some inconsistencies in the small particle size region for Fe and Ru catalysts, i.e., an opposite activity trend and an abnormal peak TOF value were observed on a Fe catalyst and a Ru catalyst (2 nm), respectively. Further study from the literature provides deeper insights into the catalyst behaviors. The intrinsic activity of Fe catalysts (10 nm) at 260–300 °C is estimated in the range of 0.046–0.20 s−1, while that of the Co and Ru catalysts (7–70 nm) at 220 °C are 0.1 s−1 and 0.4 s−1, respectively.