This research evaluated the effect of fermentation with Lactobacillus plantarum 11122, Lactobacillus casei 23184, and Lactobacillus lactis 1011 on structure, pasting, and in vitro digestion properties of glutinous rice starch varying in TN and HY genotype, respectively. The results showed that fermentation decreased the weight-average molecular weight and increased the radius of gyration. The short chain was increased by degrading the medium chain (B2, DP 24−35) of amorphous in starch, which directly led to the increase of branching degree and rearrangement of the starch chain. LAB fermentation increases the short-range ordered structure, helix structure, and crystallinity by polymerization or interactions of short chains between intermolecular and intramolecular. Furthermore, the pasting characteristic of the fermented starch sample obtained obvious improvement in terms of hydration capacity, including breakdown and setback value. Fermentation facilitated the forming of both slowly digestible starch (17.1–30.79%) and resistant starch (32.3–46.8%) in TN but caused a decline in the content of rapidly digestible starch (25.47–43.6% in TN, 9.36–17.8% in HY). The result of Pearson’s correlation tests and PCA showed the variety of structural and physicochemical of fermentation-treated starch depend highly on the starter culture and starch resources. These results provided new data support for the potential application of modified starch by fermentation with LABs.