Rhodopseudomonas palustris WP3-5 accumulated PHB in growth phase, and PHB could be utilized as another carbon and energy source when its content reached maximum value. Microorganism ceased growing when nitrogen source was exhausted, and used excessive energy to produce more hydrogen in the stationary phase. Rps. palustris WP3-5 could not synthesize PHB under low concentration of carbon source because substrate was degraded rapidly, and there were no difference of hydrogen production between wild-type strain and its PHB synthase-deficient mutant Rps. palustris M23. When concentration of carbon source was three times higher, cumulated hydrogen volume and substrate conversion efficiency of Rps. palustris WP3-5 were better than Rps. palustris M23. This result coincided with other experiments in different culture conditions. But when using malate as carbon source, Rps. palustris WP3-5 had lower substrate degrading rate and cumulated hydrogen volume, and PHB was not accumulated. Rps. palustris WP3-5 used most energy to produce hydrogen in the stationary phase and PHB content was below 10% cell dry weight, accounting for less than 5% of the substrate electrons utilized. This portion of energy might partially be redistributed to synthesize soluble microbial product (SMP). Therefore, the competition relationship between hydrogen production and PHB accumulation was insignificant.