Klebsiella pneumoniae, capsulated bacterium, is an important industrial microorganism. Roles of the Rcs phosphorelay system on K. pneumoniae capsular polysaccharide synthesis were investigated in this work. In this research, rcsA and rcsB in K. pneumoniae were knocked out individually with the Red recombinase assisted gene replacement method. Capsule synthesized by K. pneumoniae ΔrcsA and K. pneumoniae ΔrcsB were both weak, therefore the transformation efficiency of cells was significantly increased. When these two strains were cultured with glucose or glycerol as a main carbon source, the yields of 2,3-butanediol or 1,3-propanediol produced by the cells were both higher than that of the wild-type strain. Cells of the two strains were more likely to agglutinate in the broth, which is favored for the downstream process. rcsA and rcsB over-expression strains were constructed, and the growth of the two strains were both slower than the wild-type strain. The transformation efficiency of rcsA and rcsB over-expressing strains both decreased compared with the wild-type strain. The titer of extracellular polysaccharide and the viscosity of fermentation broth of rcsA or rcsB over-expression strains increased. Especially, 10.33 g/L of extracellular polysaccharide was produced by the rcsA over-expression strain, which was five times of that of the wild type strain. On the whole, the regulation of rcsA and rcsB expression provides a novel way to influence the performance of K. pneumoniae.