Background Accumulating evidence suggests a critical role of intestinal dysbacteriosis in surgical site infections and anastomotic leakage after abdominal surgery. However, a direct correlation between pre-existing dysbacteriosis and postoperative infectious complications has not yet been established clinically. Methods A total of 353 consecutive patients who underwent colorectal cancer (CRC) surgery were enrolled. Gram-stained faecal smears were tested at admission and the first defecation after surgery. Intestinal dysbacteriosis was graded into three groups: normal or slightly decreased intestinal microflora (grade 1), moderate dysbacteriosis (grade 2), and severe dysbacteriosis (grade 3). Clinical outcomes were postoperative infections and anastomotic leakage within 30 days after surgery. Results At the preoperative assessment, 268 (75.9%) patients had normal or slightly decreased intestinal microflora, 58 (16.4%) patients had moderate dysbacteriosis, and 27 (7.6%) patients had severe dysbacteriosis. The patients with preoperative dysbacteriosis had a higher rate of early postoperative diarrhoea (grade 2: OR = 4.53, 95% CI 2.28–9.00, grade 3: OR = 4.52, 95% CI 1.81–11.31), total complications (grade 3 40.7% vs. grade 2 25.9% vs. grade 1 12.7%, P < 0.001), and anastomotic leakage (grade 3 11.1% vs. grade 2 5.2% vs. grade 1 1.5%, P = 0.002). An interaction effect among preoperative dysbacteriosis and early postoperative diarrhoea on total complications was observed in rectal cancer patients (P for interaction = 0.007). Conclusions An imbalance of the intestinal microbiome exists in a considerable proportion of CRC patients before surgery. Preoperative dysbacteriosis is associated with higher rates of early postoperative diarrhoea, which further correlates with infectious complications and anastomotic leakage. However, the contribution of preoperative dysbacteriosis to the occurrence of anastomotic leakage needs to be clarified in further studies. Trial registration ChiCTR, ChiCTR1800018755. Registered 8 October 2018—Retrospectively registered, http://www.chictr.org.cn/ChiCTR1800018755.