ObjectiveTo explore the variation of the structure of the intestinal flora between healthy people and patients with obstructive jaundice perioperatively. MethodsFrom February 2013 to August 2014, 20 patients with obstructive jaundice and 10 healthy persons (normal control group) in our hospitol were selected as the research object. The first stool specimens of the research object after admission were obtained and the total fecal bacteria DNA were extracted. After polymerase chain reaction amplification, the changes in the structure of bacterial flora were dynamic observed by using denaturing gradient gel electrophoresis (DGGE), and the gel bands were analyzed by using Quantity One software. The similarity and diversity of flora structure, and principal component analysis (PCA) were analyzed. ResultsSignificant differences of colonic microflora were found between patients with obstructive jaundice and healthy people; advantage intestinal flora in obstructive jaundice patients was significant lower than the normal control group. With the extension of time and degree of obstruction aggravated, a descending trend was found in number, abundance, and diversity of the intestinal microflora (P < 0.05). ConclusionThere is significant differences in the structure of colon bacteria in patients with obstructive jaundice and healthy persons.