The study investigated the preparation of set yoghurts by adding three common commercial polysaccharide stabilizers, namely sodium alginate (SA), gellan gum (GG), and konjac gum (KGM), in milk fermentation to evaluate their effects on the texture, rheology, and microstructure of set yoghurts. The physicochemical properties, water-holding capacity (WHC), texture, low-field nuclear magnetic resonance (LF-NMR), rheology, and microstructure of set yoghurts added with different kinds and quantities of polysaccharides were compared and analyzed. The results showed that the set yoghurts added with anionic polysaccharide GG had more obvious effects on improving WHC, firmness, and rheological properties compared with the set yoghurt added with KGM and SA. The firmness of set yoghurts with 0.02% (w/v) GG increased from 1.17 N to 1.32 N, which significantly improved the gel structure. The transverse relaxation time (T₂) of set yoghurts added with GG was the closest to that of the control. Compared with the set yoghurts added with 0.02% SA and KGM, the free water area (A₂₃) of the one added with 0.02% GG decreased most significantly. Moreover, all samples showed shear-thinning behavior, and the apparent elastic and viscous modulus (G′, G″) increased with the increase of GG concentration. The G′ and G″ of set yoghurts with 0.005% SA and KGM were higher than those in the control, decreased when adding 0.010%, and then increased with the increase of SA and KGM. Additionally, the microscopic observation demonstrated that the addition of GG in set yoghurts significantly promoted the formation of larger protein clusters and showed a tighter and more uniform protein network comparing with the other two polysaccharides (SA, KGM).