Saponins from Momordica charantia L. are a class of triterpenoid glucoside molecules that contribute to the bitter flavour of the plant and possess pharmacological properties. However, little is known about how the bioactivity and bitter flavour of saponins are affected by thermal processing. We established saponin profiles in bitter gourd extracts using a UPLC-ESI-MS/MS method. Seven saponins including momordicoside F₁, momordicoside F₂, momordicoside I, momordicoside K, momordicoside L, 3β,7β,25-trihydroxycucurbita-5, 23(E)-dien-19-al, and momordicine I were monitored for the effects of thermal processing on their stabilities. The results showed that both 3β,7β,25-trihydroxycucurbita-5,23(E)-dien-19-al and momordicoside L were extremely sensitive to heat treatment, particularly when they were heated at 100°C for more than 10 mins and under 121°C for 20 mins. Other saponins were reduced significantly by autoclaving, but they remained unchanged at lower temperatures. In conclusion, specific bitter gourd saponins are affected by thermal treatment, which may modify the bioactive components or bitter flavour of the bitter gourd extracts.