In order to study the relationship between pepper (Capsicum annuum) cytoplasmic male sterility and SDH4， we cloned a key enzyme gene of mitochondrial electron transfer complex Ⅱ. SDH4 gene by using specific primers to amplify the mitochondrial genome sequence reported by GenBank. By analyzing the spatiotemporal expression of SDH4 gene and transcriptional editing site to find differences of male sterile line and maintainer line. The results showed that: (1) the length of the coding region of the target gene in two lines was 378 bp, encoding 125 amino acid residues. (2) SDH4 gene has a different expression in different tissues in pepper maintainer line, the highest in seed and the lowest in stem. (3) There is a difference of SDH4 gene expression in the same period of budding development of different materials. SDH4 gene in meiosis stage of pollen mother cell of male sterile line was significantly lower than that of maintainer line, in the other three periods (sporogenous cell division stage, uninucleate microspore stage and mature pollen stage), SDH4 gene expression of male sterile line were higher than those of maintainer line. (4) In male sterile line, the RNA editing of SDH4 gene at the 29 site resulted in the change of amino acid from serine to leucine, which enhanced the hydrophobicity of the protein structure. It is considered that the difference of SDH4 gene expression in pepper cytoplasmic male sterility line 9704A and maintainer line 9704B may cause abnormal energy metabolism supply of plants, resulting in male sterility.