FeCrAl monolith catalysts are suitable for high-flux low-temperature Fischer-Tropsch synthesis (LT-FTS) due to their high thermal conductivity and low pressure drop at high gas hourly space velocity (GHSV). In this study, the reaction and thermal performance of the catalysts with increasing Co-loading (MCINC) and decreasing Co-loading (MCDEC) at different GHSV were studied by experiment and numerical simulation. The results showed that the reaction performance of MCDEC was slightly better than that of MCINC at 28000 h−1, while the thermal performance of MCDEC was much better than MCINC. The reason was explained by the heat transfer mechanism. The dominant heat transfer mode turned to the axial convective heat transfer at 28000 h−1. The powerful axial convective heat transfer improved the transfer of the reaction heat toward the outlet and decreased the temperature of MCDEC. Conversely, it exacerbated the heat accumulation near the outlet of MCINC. Therefore, MCDEC was more suitable than MCINC for the better thermal management of high-flux LT-FTS. These results demonstrated that designing the axial gradient of Co-loading according to the GHSV is a promising approach for the thermal intensification in LT-FTS.