The differential screening method was used to isolate the soy photoperiodic response-related genes and to further elucidate the molecular mechanisms of the soybean photoperiodic response. The light-sensitive species Zhong Dou 24 was used to receive long-time sunshine, short-time sunshine, and natural sunshine treatment. The cDNA-amplified fragment length polymorphism technique was used to screen the differentially expressed cDNA fragments. The rapid amplification of cDNA end technique was used to isolate the gene. Semi-quantitative reverse transcription polymerase chain reaction analysis was used to analyze the gene expression patterns in different light cycles. The gene had a total length of 983 bp, contained a complete open reading frame that encoded 248 amino acids, and shared homology with the mitochondrial phosphate transporter protein. The expression pattern analysis results showed that this gene was expressed in the early stages of soybean growth and development. The short-time sunshine inhibited its expression, whereas the long-time sunshine enhanced its expression. The differential screening method was used to isolate the soybean mitochondrial phosphate transporter gene. The gene may be used as a negative regulatory factor that is involved in the photoperiodic response of soybean.