The purpose of this study was to review the differential expression of intestinal microbiota in colorectal cancer (CRC) with quantitative real-time PCR (q-PCR). An online search within PubMed, Web of Science and Wanfang Database up to June 6, 2015 was conducted. We used an original assessment tool to assess the quality of included articles. A systematic review and meta-analysis described the altered intestinal microbiota in colorectal cancer versus healthy control (HC). Six articles, involving 192 CRC patients and 264 healthy controls were included. Scores of quality assessment of these articles ranged from 7 to 16. Significant differences of microbial expression in CRC compared with HC were found in Bifidobacterium (SMD=-3.303, P=0.048), Faecalibacterium prausnitzii (SMD=-0.33, P=0.018) and Enterobacteriaceae (SMD=2.69, P=0.009), while total bacteria, Lactobacillus, Bacteroides-Prevotella group and Escherichia coli failed to display significant difference. We can conclude that there is down regulation of some colonization bacteria such as Bifidobacterium and Faecalibacterium prausnitzii, and up regulation of Enterobacteriaceae in CRC. Microbiota changes also participate in the pathogenesis of CRC.