<p>Coconut milk agar based jelly (CMJ) is a dessert widely consumed in Thailand and many Asian countries. To meet the market need for reducing sugar and calorie intake, the objective of this study was to investigate the effect of sucrose substitutes on the physicochemical, thermal and microstructure properties of this product. Varied ratios of each sugar alcohol (maltitol, sorbitol and isomalt) combined with Rebaudioside A (50:50, 60:40, 70:30, 80:20, 90:10) with the amount based on their equivalent sucrose sweetness intensity were used for sucrose substitution. It was found that replacing sucrose with these alternative sweeteners significantly affected the whiteness index (WI), hardness, chewiness, water activity and syneresis of CMJ (<i>p ≤ 0.05</i>). The WI, hardness, chewiness, water activity and syneresis of CMJ significantly decreased with increasing proportion of sugar alcohols (<i>p ≤ 0.05</i>). The CMJ with isomalt and rebaudioside A substituted at a ratio of 50:50 had the closest textural (hardness and chewiness) and thermal properties (temperature and enthalpy of gel setting and melting) (<i>p &gt; 0.05</i>) with microstructure similar to that of the control sample. These findings suggest the potential for the use of combined sweeteners to develop low sugar and calorie agar-based jelly in the confectionery and sweet industry.</p>