The conductivity of carbon nanotube (CNT)/polymer nanocomposites is known to be influenced by post-processing treatment. For example, annealing can greatly increase the conductivity. However, the effect of cooling rate in this process has been largely ignored. In this work, we demonstrated the remarkable influence of cooling rate on the conductivity in the CNT/polypropylene (PP) nanocomposites apart from annealing. CNT/PP nanocomposites with various CNT concentrations were prepared by melt processing using a micro-compounder. After compression molding, the nanocomposites were cooled down with a fast and a slow cooling rate (150 vs. 1.5 °C/min) respectively. A slow cooling rate significantly boosted the conductivity of the CNT/PP nanocomposites, and the percolation threshold was greatly reduced from 0.43 vol.% to 0.21 vol.% CNT. The conductivity decreased with decreasing the slow cooling starting temperature, and a significant drop in conductivity was observed when the slow cooling process started from 140 °C which is close to the onset crystallization temperature of PP. Annealing processing can suppress this conductivity reduction but only before the PP crystallization onset temperature. These results indicate that the formation of CNT conductive pathways in the CNT/PP nanocomposites after processing are controlled both by annealing and cooling (crystallization) process. The higher conductivity in the CNT/PP nanocomposites with a slow cooling rate is attributed to the enhanced volume exclusion effect which is promoted by the lower PP crystallization kinetics, the larger crystal size and the higher degree of crystallinity.