The non-isothermal degradation of two cyanidin-based anthocyanins, cyanidin-3-glucoside and cyanidin-3-rutinoside, was investigated in aqueous system within the temperature range from 100 to 165 °C, and the degradation kinetics was modelled using Monte Carlo simulation. The two anthocyanins showed different stability, with cyanidin-3-glucoside exhibiting a higher degradation rate than cyanidin-3-rutinoside. The derived degradation rate at the reference temperature of 132.5 °C and activation energy of cyanidin-3-glucoside and cyanidin-3-rutinoside were 0.0047 and 0.0023 s(-1), and 87 and 104 kJ/mol, respectively. The antioxidant capacity of the thermally processed anthocyanins solutions was measured by using ABTS and DPPH assays. Results showed that the antioxidant capacity of the samples remained at the same level during the thermal treatment process under various conditions, i.e., there was no significant difference (P>0.05) in the antioxidant capacity amongst the samples despite their significantly different contents of the two anthocyanins.