Background: Intestinal Fusobacterium nucleatum (F. nucleatum) infection has been implicated into the progression of colorectal cancer (CRC). However, F. nucleatum as a biomarker in 5-fluorouracil (5-FU) resistance of CRC has not been fully analyzed by comparing with other types of gut microbiota. This meta‑analysis aimed to compare the diagnostic performance of intestinal Fusobacterium nucleatum, Bacteroides fragilis and Escherichia coli in 5-FU resistance to colorectal cancer and provide evidence‑based data to clinical practice. Methods: Comprehensive searches of PubMed, Embase, Cochrane Library and Web of Science databases were conducted by the following key words: “Fusobacterium nucleatum”, “5-Fluorouracil resistance”, “Bacteroides fragilis”, “Escherichia coli” and “colorectal cancer(s)”. A total of 11 studies were selected according to the preestablished inclusion and exclusion criteria and analyzed by Review Manager 5.4 software. The sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR) and their corresponding 95% confidence interval (CI) of each eligible study were summarized. Results: Overall sensitivity and specificity of F. nucleatum detection in 5-FU resistance of CRC were 0.65 (95% CI:0.60-0.69) and 0.70 (95% CI:0.59-0.87), respectively. Its PLR and NLR in detecting colorectal cancer were 2.57 (95% CI:1.47-3.21) and 0.52 (95% CI:0.43-0.63). DOR value was 4.92 (95% CI:2.23-7.33), which significantly exceeds the performance of B. fragilis (DOR: 0.53, 95% CI:0.31-0.82) and E. coli (DOR: 0.63, 95% CI: 0.57-0.76) for indicating 5-FU resistance of CRC. Conclusion: Compared with B. fragilis and E. coli, intestinal F. nucleatum is a valuable biomarker for 5-FU resistance to colorectal cancer.