Low glycaemic index (GI) foods minimize large blood glucose fluctuations and have been advocated to enhance fat oxidation and may contribute to weight management. We determined whether the inclusion of isomaltulose compared to sucrose in a low/high GI meal sequence can modulate the glycaemic response and substrate oxidation in an Asian population. Twenty Chinese men (body mass index (BMI): 17-28 kg/m²) followed a 24 h low GI (isomaltulose, PalatinoseTM) or high GI (sucrose) diet in a randomized double-blind, controlled cross-over design. Treatment meals included dinner (day 1), breakfast, lunch, and snack (day 2). Continuous glucose monitoring provided incremental area under the curve (iAUC) and mean amplitude of glycaemic excursion (MAGE) and 10 h indirect calorimetry (whole body calorimeter) (day 2) provided energy expenditure and substrate oxidation. Our results demonstrated that the low GI diet resulted in lower 24 h glucose iAUC (502.5 ± 231.4 vs. 872.6 ± 493.1 mmol/L; p = 0.002) and lower 24 h glycaemic variability (MAGE: 1.67 ± 0.53 vs. 2.68 ± 1.13 mmol/L; p < 0.001). Simultaneously, 10 h respiratory quotient increased more during high GI (p = 0.014) and fat oxidation was higher after low GI breakfast (p = 0.026), lunch (p < 0.001) and snack (p = 0.013). This indicates that lower GI mixed meals incorporating isomaltulose are able to acutely reduce the glycaemic response and variability and promote fat oxidation.