Purpose <p>To evaluate the effects of a plant-based milk with fermented brown rice on constipation symptoms in patients with functional constipation and to identify post-intervention gut microbial alterations that may underlie potential mechanisms.</p> Methods <p>This is a randomized controlled trial among 100 participants with functional constipation. Participants were randomly assigned to the intervention group (plant-based milk with fermented brown rice, 2 bottles/day, 500&#xa0;ml in total), or the control group (an isocaloric plant protein milk, equivalent dose) for 3 weeks. The primary outcome is complete spontaneous bowel movement (CSBM) rate, while secondary outcomes include score of individual symptoms assessment of constipation, bowel movement frequency (BMF), and gut microbial changes (metagenomics).</p> Results <p>A total of 99 participants completed the intervention. CSBM and BMF increased, and GSRS scores decreased over time in both groups, with no significant between-group differences. The plant-based milk with fermented brown rice relieved constipation symptoms more than the control group did, with significant between-group differences in straining, bloating and abdominal pain (all <i>P</i> &lt; 0.05). The intervention group showed increases in 8 species, including three beneficial species in the genus <i>Blautia</i>, associated with relief of abdominal pain after the intervention. Meanwhile, machine learning models identified gut microbiota features predicting intervention responders.</p> Conclusion <p>Our study did not find between-group difference in CSBM, while the plant-based milk with fermented brown rice showed greater effectiveness in relieving constipation symptoms and optimizing gut microbiota. Functional species benefiting intestinal health in response to the intervention were also identified.</p> Clinical trial registry <p>This study has been registered in the Chinese Clinical Trial Registry (https://www.chictr.org.cn/, ChiCTR2400088688).</p>