This study designed a new programmed temperature control (PTC) process for cooked chicken, aiming to increase the efficacy of Clostridium perfringens spore inactivation through inducing spore germination at different levels of dormancy. The results showed that the use of PTC treatment in the presence of germinant AGFK (a mixture of l-asparagine, D-glucose, D-fructose, and KCl) lead to a reduction of exceeding 6 lg CFU/mL spores in a model system after being subjected to 90 °C for 20 min. A significant up-regulation of gerKA, gerKC and gerAA relative expression suggested that the PTC treatment may induce more spore germination. Meanwhile, there was an observed rise in the release of pyridine-2,6-dicarboxylic acid, accompanied by a steady decline in refractivity. In the cooked chicken meat undergone a cooling process, the number of C. perfringens spores were reduced by approximately 5 lg CFU/g after the PTC treatment and heated at 90 °C for 20 min. In conclusion, the PTC treatment can effectively enhance the inactivation of C. perfringens spores by inducing more spore germination at different levels of dormancy during cooked meat preparation.