The invention discloses a marking method of applying an SSR molecular marker technology on a peony for oil. The method comprises the following steps: designing primers, extracting peony genome DNA, carrying out amplification reaction, testing polyacrylamide gel electrophoresis and the like. According to the marking method, a microsatellite fragment is amplified by PCR reaction, the amplified product is subjected to gel electrophoresis testing, strips are rich, isotopes are not used, the experimental process has the effects of being simple, practical, short in consuming time and low in cost, moreover, the method has a great number of markers, and the markers are randomly distributed in an animal and plant whole genome; allelic loci of each marker have relatively high polymorphism and high polymorphism information content; the markers are inherited in a Mendel way, and are co-dominant markers; the experiment operation process has no high requirements on the quality of DNA, the use amount of the DNA is less, the reliability is good, and the repeatability is good; the method is suitable for amplification of the SSR molecular markers for peony genus for oil; a silver staining method in polyacrylamide gel electrophoresis is improved, both time and cost are saved, and the efficiency of applying the SSR molecular markers on the peony genus is further improved.