Heat treatment is a widely applied technique in the preservation of fruits and vegetables, effectively addressing issues such as disease management, rot prevention, and browning. In this study, we investigated the impact of heat treatment at 35 °C for 24 h on the quality characteristics and disease resistance of two sweet potato varieties, P32/P (Ipomoea batatas (L.) Lam. cv ‘Pushu13’) and Xinxiang (Ipomoea batatas (L.) Lam. cv ‘Xinxiang’). The growth in vitro and reproduction of Rhizopus stolonifer were significantly inhibited at 35 °C. However, it resumed when returned to suitable growth conditions. The heat treatment (at 35 °C for 24 h) was found to mitigate nutrient loss during storage while enhancing the structural characteristics and free radical scavenging capacity of sweet potato. Additionally, it led to increased enzyme activities for APX, PPO, and POD, alongside decreased activities for Cx and PG, thereby enhancing the disease resistance of sweet potato against soft rot. As a result, the heat treatment provided a theoretical basis for the prevention of sweet potato soft rot and had guiding significance for improving the resistance against sweet potato soft rot.