Three low molecular weight (LMW) sweeteners (D‐tagatose, erythritol, and trehalose) were studied in yoghurt formulations to investigate their effects on syneresis, rheological properties, water distribution, and microstructural characteristics. The results indicated that trehalose improved syneresis, the fermentation process, and rheological properties compared to yoghurt fortified with sucrose, while D‐tagatose and erythritol demonstrated the opposite effects on fermentation. With the addition of LMW sweeteners, the apparent viscosity and frequency sweep of yoghurt increased, with trehalose showing a better effect than sucrose or the other two LMW sweeteners. The water distribution, as indicated by T2 relaxation time, was also significantly improved with trehalose. Electron microscopy results showed that the three LMW sweeteners decreased the porous structure of the yoghurt gel and enhanced protein aggregation, leading to a denser network. Fourier‐transform infrared spectroscopy results demonstrated that trehalose increased the disorder of hydrocarbon chains, the vibrations of N–H and C–N groups, and the C–O stretching, promoting the formation of casein/trehalose complexes, which improved the gel syneresis of yoghurt containing trehalose. Those results suggest that trehalose could be used as a novel sweetener to replace sucrose in dairy products.Practical ApplicationThis study investigated the rheological, gel syneresis, water distribution, and microstructural properties of yoghurt with three LMW sweeteners and found that yoghurt supplemented with trehalose significantly improved syneresis and the structure of casein micelles through increased hydroxyl groups. Trehalose can potentially be used trehalose as a yoghurt stabilizer for dairy production, enhancing gel syneresis properties.