Background: Functional constipation is a common disorder of gut-brain interaction that substantially affects bowel function, psychological well-being, and quality of life. Probiotic supplementation represents a microbiota-targeted nutritional strategy for functional constipation, but associated host-response signals remain incompletely understood. Methods: This single-center, randomized, double-blind, placebo-controlled trial enrolled 104 adults who met the Rome IV criteria for functional constipation. Participants received either Results: Probio87 supplementation significantly increased weekly complete spontaneous bowel movements compared with placebo at Week 8 and Week 12. Improvements were also observed in Rome IV symptom scores, constipation-related quality of life, and HAMD-24 domains related to anxiety, sleep, and retardation. Exploratory whole-blood gene-expression analysis showed differential host-response signals after intervention, characterized by increased BDNF expression and reduced expression of IL-1β, CD117, CXCR5, IDO1, DBH, and MLNR in the probiotic group relative to placebo. No intervention-related adverse events or clinically relevant abnormalities in hematological, hepatic, or renal safety parameters were observed. Conclusion: Clinical trial registration: https://www.chictr.org.cn/showproj.html?proj=205514, identifier (ChiCTR2300075360).