Spinnable mesophase pitches C-MP, P-MP, and C/P-MP were synthesized from coal tar pitch, petroleum pitch, and their cocarbonized pitches, respectively. The molecular structures of these mesophase pitches and their effect on the microcrystalline sizes of the mesophase and the properties of carbon fibers derived from them were comparatively investigated. The molecular structures and orientation of the prepared mesophase pitches have significant influence on the performance of resultant carbon fibers. In comparison with P-MP and C/P-MP, C-MP possessing the highest aromaticity, a rigid molecular structure, and a very small amount of methyl groups makes C-MP-CFs with smaller crystal size and lower decomposition during the preparation process and thus results in the best mechanical properties of their carbon fibers, consequently. The prepared P-MP, however, containing abundant methyl groups and possessing a semirigid molecular structure, yields products with higher d(002)-spacing and larger mesomorphic phase size. The largest crystallite dimension of P-MP combined with its higher molecular orientation makes P-MPCFs possessing the highest crystal size and axial thermal conductivity. On the other hand, C/P-MP shows the molecular structure character of both coal tar pitch and petroleum pitch and a tunable mesophase domain orientation. The carbon fiber prepared from cocarbonized C/P-MP shows both good mechanical properties, like C-MP-based fiber, and, in particular, ultrahigh thermal conductivity, like P-MP-based fiber.