Crohn's disease (CD) is a chronic inflammatory bowel disease characterized by periods of remission and relapse. Probiotics have been suggested as potential therapeutic agents for managing CD, but their effects on clinical outcomes remain unclear. This meta-analysis aimed to evaluate the efficacy and safety of probiotics in patients with CD. A systematic search was conducted across multiple databases, including Medline, Embase, Cochrane Library, Wanfang, and CNKI. Randomized controlled trials (RCTs) assessing probiotic interventions in patients with CD were included. The primary outcomes were clinical remission and relapse, while secondary outcomes included endoscopic recurrence and safety. Risk ratios (RR) and 95 % confidence intervals (CIs) were calculated using a random-effects model. Sixteen RCTs involving 1112 patients were included. Probiotics significantly increased the likelihood of clinical remission in patients with active CD (RR: 1.27, 95 % CI: 1.09-1.47, p = 0.002) with mild heterogeneity (I(2) = 16 %). However, no significant effect on clinical relapse was found in patients in remission (RR: 0.93, 95 % CI: 0.68-1.28, p = 0.66). In addition, probiotics did not reduce the risk of endoscopic recurrence after ileocecal resection (RR: 0.86, 95 % CI: 0.63-1.18, p = 0.34), and the incidence of severe adverse events was comparable between patients receiving probiotics and controls (p = 0.82). Probiotics may help enhance clinical remission in active CD patients possibly by modulating gut microbiota. However, no significant effect on relapse or endoscopic recurrence in remission was observed.