This study aimed to systematically review the clinical efficacy of probiotics or synbiotics supplementation in the treatment of chemotherapy-induced complications and gut microbiota dysbiosis in patients with gastrointestinal cancer. A literature search was performed systematically using PubMed, Embase, Cochrane, Web of Science, Wanfang Data, and CNKI for randomized controlled trials of probiotics or synthetic supplementation on chemotherapy-induced complications and gut microbiota dysbiosis in gastrointestinal cancer up to December 2023. The outcome measures included chemotherapy-related complications and the the incidence of gut microbiotas. Fifteen studies were finally eligible for meta-analysis, involving 1356 patients. Meta-analysis results showed that the the incidence rates of chemotherapy-related complications such as nausea and vomiting [RR = 0.61, 95% CI (0.46,0.82), P = 0.0008] and diarrhea [RR = 0.47, 95% CI (0.32,0.68), P < 0.001] were significantly reduced after probiotic intervention. The number of intestinal flora changed significantly after intervention, such as bifidobacterium [SMD = 1.33, 95% CI (0.52,2.31), P = 0.001], Escherichia coli [SMD = -0.82, 95% CI (-1.26, -0.38), P = 0.0003], and the difference was statistically significant. Probiotics or synbiotics supplementation can reduce chemotherapy-induced complications in patients with gastrointestinal cancer and regulate the number of gut microbiotas to balance the intestinal microecology of the body.