In this study, the glycerol metabolism by Klebsiella pneumoniae is stoichiometrically analyzed according to energy (ATP), reducing equivalent and product balances. The theoretical analysis reveals that a microaerobic condition is more perfect for the production of 1,3-propanediol (1,3-PD) from glycerol by K. pneumoniae than anaerobic and aerobic conditions. The yields of 1,3-PD, biomass and ATP to glycerol under microaerobic conditions depend not only on the molar fraction of reducing equivalent oxidized completely by molecular oxygen in tricarboxylic acid (TCA) cycle (δ), but also on the molar fraction of TCA cycle in acetyl-CoA metabolism. The maximum theoretical yield of 1,3-PD to glycerol could reach to 0.85mol/mol rather than 0.72mol/mol if all acetyl-CoA entered into TCA cycle instead of acetic acid pathway under anaerobic conditions. The yield of 1,3-PD is still higher than 0.72mol/mol in a range of δ between 0.11 and 0.48, which corresponds to respiratory quotient (RQ) between 11.34 and 2.66. In the same range of δ or RQ, the biomass under a microaerobic condition is more than that of an anaerobic culture. The experimental results of batch cultures demonstrate that microaerobic cultivations are favorable for cell growth, reduction of culture time and ethanol formation, and enhancement of volumetric productivity of 1,3-PD. In addition, no aeration could improve the yield of 1,3-PD to glycerol in comparison with that of an anaerobic or aerobic culture.