K. pneumoniae CGMCC1.9131 was isolated and found to be far more excellent than other strains reported for the 1,3-propanediol (PDO) production. Genetic modifications were carried out to enhance the productivity and facilitate the purification processing of PDO. D-lactate dehydrogenase and capsular polysaccharides encoding genes were deleted in the engineered K. pneumoniae. The PDO productivity was increased and the concentration of lactate decreased dramatically from more than 40 g/ L to <3 g /L. Culture filtration and electrodialysis in the purification processing were greatly facilitated. Engineered stains also shown a better tolerance to the high glycerol in the medium. The engineered stains were valuable for the industrial production.