The growth of carbon nanotubes (CNTs) in a flame requires conditions that are difficult to achieve in a highly heterogeneous environment. Therefore, the analysis of the properties of the reaction zone within the flame is critical for the optimal growth of CNTs. In the present study, a comprehensive comparison between the CNT synthesis using a methane diffusion flame and a premixed flame is conducted regarding the morphology and crystallinity of the as-grown nanotubes. The premixed burner configuration created a flame that is stabilized through axisymmetric stagnation flow through sintered metal with one-dimensional geometry, different from a conventional co-flow flame. The significant difference in temperature distribution between the two flames causes a difference in the characteristics of the growth products. In the diffusion flame, the growth is limited to specific regions at certain height-above-burner (HAB) values with a temperature range of 750 to 950 °C at varying radial locations. The identified growth regions at different HAB values showed similar temperature distributions that yield CNTs of similar characteristics. Interestingly, the growth of CNTs in the premixed flame is dictated by only the HAB because the temperature distribution is relatively uniform along the radial directions but significantly different in the vertical direction. 17.3% variation in temperature in the axial direction successfully led to 44% and 66% variation in CNT diameter and crystallinity, respectively. The morphology control capability demonstrated in the present study is important for CNT functionalization for energy storage, nanosensor, and nanocomposite applications, where diameter and crystallinity are influential properties that govern the overall performance of the components.