The main objective is to effectively denature the autolysis enzymes of C. frondosa on the premise of avoiding the quality deterioration caused by overheating. The effects of the different thermal treatments (blanching at 40–80 °C for 45 min, boiling and steaming at 100 °C for 15–120 min) on the cooking yield, moisture content, protein degradation, texture, and enzyme inactivation were studied, and the inner relationship was investigated by multivariate analysis. The autolysis enzymes of C. frondosa were thermally stable and cannot be denatured completely by blanching. Boiling and steaming could efficiently inactivate the enzymes but overheating for 60–120 min reduced the cooking yield and texture quality. Boiling at 100 °C for 45 min was suitable for pre-treatment, with cooking yield of 70.3% and protein content of 78.5%. Steaming at 100 °C for at least 30 min was preferable for long-term storage and instant food, in which the relative activity was only 3.2% with better palatability.