The method of metabolic pathway stoichiometry was used to analyze the fermentation of glycerol to 1,3-propanediol by Klebsiella pneumoniae DSM 2026, with particular emphasis on the regulation of hydrogen formation and balance of reducing equivalents (NADH2). Under conditions of glycerol limitation, H-2 formation was found to be higher than the maximum amount that could be generated from the splitting of pyruvate to acetyl-CoA. Simultaneously, a lower recovery of reducing equivalents was found in the reduced product 1,3-propanediol. Under conditions of glycerol excess, formation of H-2 was drastically reduced and a surplus of NADH2 was generated for the formation of 1,3-propanediol. These findings indicate the existence of enzymes in K. pneumoniae that transfer reducing equivalents from NADH2 to H-2 and 1,3-propanediol flexibly. The physiological meanings of these regulatory mechanisms are discussed from the viewpoint of bioenergetics and product inhibition. Taking these regulation mechanisms into account, the maximum energy and product yields of this fermentation were calculated, which agreed well with experimental results. A corrected NADH2 balance equation was derived which can be used to calculate the formation of hydrogen under different conditions.