The invention discloses a method for assistantly sieving soybean with lower plant height trait and a special primer thereof. The method comprises the following steps: the genomic DNA of soybean to be tested is adopted as a template, the primer is used for carrying out PCR amplification on a party A and a party B respectively and an amplified product of the soybean to be tested is obtained; the genomic DNA of Charleston is adopted as a template, the primer is used for carrying out PCR amplification on the party A and the party B respectively and an amplified product of the Charleston is obtained; carrying out electrophoresis on the amplified products of the soybean to be tested and the Charleston, if presenting same band type, the soybean to be tested is candidate soybean with lower plant height trait; a primer pair A consists of nucleotides shown in a sequence 1 of a sequence table and a sequence 2 of the sequence table; and a primer pair B consists of nucleotides shown in a sequence 3 of the sequence table and a sequence 4 of the sequence table. The invention also provides a quantitative trait locus of the soybean with height plant, which is positioned at an L linkage group and is positioned between Sat_009 and Sat113 of the SSR primer locus. The method can judge whether the quantitative trait locus (QTL)-htL_1 is contained by DNA measurement of soybean variety resource or filial generation, thus predicting the plant height level of the soybean and accelerating and improving breeding speed of the plant height of the soybean.