Abstract: A SEC12-like protein gene CPU1 and application thereof in improving soybean phosphorus efficiency are disclosed. Through genome-wide association studies, a major genetic locus affecting soybean phosphorus efficiency is identified, and the candidate gene CPU1 is discovered and validated. There are natural variations in gene CPU1 in soybean population, including two alleles, phosphorus-inefficient allele CPU1-H1 and phosphorus-efficient allele CPU1-H2. Studies based on CPU1-transformation plants shows that inhibiting the expression of the allele CPU1-H2 significantly reduces soybean phosphorus efficiency, and ultimately reduces the biomass and yield of transgenic plants. The present disclosure provides new scientific insights into genetic bases underlying natural phenotypic variation in crops, and provides novel allele resources for molecular breeding of phosphorus efficiency.