Under simulated gastrointestinal digestion, we investigated the protective and releasing effects of lotus seed cross-linked resistant starch (LSCS) with low, medium, and high cross-linking degree toward Lactiplantibacillus plantarum ACCC 11095 and associated structural changes. Probiotic microcapsules (PM) made of high crosslinking starch showed better encapsulation rates (48.81%) and released 6.26 log CFU/g of viable bacteria after digestion, which helped colonize and exert probiotic effects in the intestinal tract. Scanning electron microscopy and Fourier Transform Infrared spectroscopy confirmed better high crosslinking starch protection for probiotic bacteria. This was closely related to PM embedded materials. Correlation analysis showed that agglomeration between high crosslinking starch starch granules in PM was significantly enhanced, and amorphous zones were hydrolyzed to a lesser extent, providing better Lactiplantibacillus plantarum ACCC 11095 protection. Thus, high crosslinking starch demonstrated potential as an oral probiotic carrier in terms of cost, suitability for functional foods, and commercialization potential.