The invention discloses lotus root starch related gene GBSS functional molecule marker primers and application. An applicant designs primers gbf3: TCGCTTCTTCCACTGCTAC, and gbr3: GAAGCGAAGTTGGTTGTCA on the basis of a newly discovered molecule marker FMGBSS-I3. The primer pair can be used for identifying the content relationship of amylopectin, amylase, total starch and total dry weight in lotus roots in an auxiliary way, and is further used for total starch breeding selection. The method can be used for selection in a young seedling stage; an important guidance effect is achieved on culturing high-starch (or low-starch), high-amylopectin (or low-amylopectin) and high-amylose (or low-amylose) lotus root varieties; the breeding speed can be accelerated; the breeding cost can be reduced; the advantages of simplicity in operation, low cost and short period are achieved; the method is suitable for being popularized and used; a fast and convenient method is provided for lotus root germ plasm resource identification and lotus root breeding selection; and the development and application values are very high.