Pickled radish (Raphanus sativus) is a traditional Asian ingredient, but the traditional method takes decades to make this product. To optimize such a process, this study compared the saponin content of pickled radishes with different thermal processing and traditional processes (production time of 7 days, 10 years, and 20 years) and evaluated the effects of different thermal processes on the formation of radish saponin through kinetics study and mass spectrometry. The results showed that increasing the pickling time enhanced the formation of saponin in commercial pickled radishes (25 °C, 7 days, 6.50 ± 1.46 mg g−1; 3650 days, 23.11 ± 1.22 mg g−1), but these increases were lower than those induced by thermal processing (70 °C 30 days 24.24 ± 1.01 mg g−1). However, it was found that the pickling time of more than 10 years and the processing temperature of more than 80 °C reduce the saponin content. Liquid chromatography–mass spectrometry (LC-MS) analysis showed that the major saponin in untreated radish was Tupistroside G, whereas treated samples contained Asparagoside A and Timosaponin A1. Moreover, this study elucidated the chemical structure of saponins in TPR. The findings indicated that thermal treatment could induce functional saponin conversion in plants, and such a mechanism can also be used to improve the health efficacy of plant-based crops.