In this paper, the effects and mechanisms of a novel two-step tomato peeling method, hot lye with a post-assistance of ultrasound, were investigated. The present work aims to improve the environmental friendliness of the conventional hot lye tomato peeling method (10% w/v, 97 °C, 45 s). The results showed that 4% (w/v) lye treatment at 97 °C for 30 s with a post-assistance of a 31.97 W/L ultrasound treatment at 70 °C for 50 s achieved a 100% peelability. In this scenario, the peeling yield and lycopene content in the peeled product were significantly higher than the peeling yield and lycopene content with the conventional hot lye peeling method. The present two-step peeling method was concluded with a mechanism of chemico-mechanical synergism, in which the hot lye functions mainly in a chemical way while the ultrasound is a mechanical process. Especially from the lye side, this work first demonstrated that the lye penetrated across the tomato skin via a pitting model rather than evenly. The findings reported in this paper not only provide a novel tomato peeling method with significant environmental benefits but also discover new clues to the peeling mechanism using hot lye.