Enantiomerically pure organosilicon compounds 3-butyn-2-ol not only play an important part in asymmetric synthesis and functional materials, but also many of them are bioactive and can be applied as silicon-containing drugs, such as (S)-3-butyn-2-ol or its derivative (S)-4-(trimethylsilyl)-3-butyn-2-ol {(S)-TMSBL} is a crucial intermediate for the synthesis of 5-lipoxygenase inhibitors. The anoxygenic phototrophic bacteria capable of reducing TMSBO to the (S)-TMSBL with high yield and ee were screened, using absolute configuration, stereoselectivity, and yield as benchmarks. 51 anoxygenic phototrophic bacteria strains were tested. We, for the first time, describe the efficient synthesis of enantiopure (S)-TMSBL, which is a crucial intermediate for the synthesis of 5-lipoxygenase inhibitors through the light-controlled asymmetric hydrogenation of TMSBO by photosynthetic bacteria Thiocapsa roseopersicina SJH001, which is a newly isolated photosynthetic bacteria strain that has the capacity to capture light energy and to generate NADPH through photosynthetic electron-transfer reactions. No oxygen or other metabolic intermediates were used, which make it easy to keep higher activities of redoxase and to separate reduced product, the reducing power of NADPH generated through photosynthesis also can be used in the reduction of exogenous substrates. A novel NADPH dependent carbonyl reductase was separated from Thiocapsa roseopersicina SJH001. The enzyme gave a single band on SDS-PAGE, which was purified through ammonium sulfate, Q-sepharose anion exchange column, gel filtration chromatography on a Superdex 200 column from cell-free extract. The molecular mass of the enzyme was about 44.5 kDa, relative enzyme activity was 449.8 U/mg, which is comparable to the previously reported carbonyl reductases from other sources. These results suggested that pH, light intensity, heat-treat biocatalysis with different temperature, substrate concentration has great influence on the enzyme activity and configuration of carbonyl reductase ((S)-carbonyl reductase and (R)-carbonyl reductase) from Thiocapsa roseopersicina SJH001. We propose a probable mechanism for light-induced asymmetric hydrogenation of TMSBO to produce (S)-TMSBL by anoxygenic photosynthetic bacteria.