It is widely recognized that direct internal reforming (DIR) solid oxide fuel cells (SOFCs) fueled by biomass are one of the eco-friendly and high-power generation methods. In existing cell configurations, however, the performance and durability degradation of SOFCs are induced by a strong endothermic dry reforming of methane (DRM). They are required to understand the fundamental thermal distribution mechanism and construct new cell configurations to relax thermal distribution effects. We performed a three-dimensional thermal distribution analysis coupled with computational fluid dynamics and chemical reactions in DIR-SOFCs with the three-cell stacking reactor model as a more practical model. As a result of the simulation for temperature distribution in each case of homogeneous and functionally graded paper structure catalysts (PSCs), we have found that the largest temperature drop occurs near the inlet in the bottom layer compared with the upper and middle layers in both cases and temperature distribution is milder in the functionally graded PSC. We also have found the importance of two-dimensional reaction rate controls in gas flow and cell staking directions to uniform temperature distribution of each layer. Furthermore, we investigated the effects of exothermic electrochemical reaction in the anode on thermal distribution.