Improvement and innovation of germplasm resources are the keys of breeding new cultivars, and the distant hybridization is an important way in improving germplasm. A new variety named “Shennong Gaotangzhe” has been promoted in recent years, which was declared as a hybrid of Sorghum, maize and sugarcane. In order to identify the real germplasm sources of “Shennong Gaotangzhe”. In this study, we used morphology, SCoT markers and GISH technology to analyze the possible genetic origin of “Shennong Gaotangzhe”. Among them, the results of preliminary identification of morphology indicated that , “Shennong Gaotangzhe” was very similar to sugarcane, maize and sorghum only based on the characteristics of roots, stems, leaves and other organs，so，it was unable to accurately distinguish “Shennong Gaotangzhe” for true hybrids. According to the cluster results of SCoT markers, 12 tested materials can be divided into three categories named I, II and III, the category I included three kinds of Sorghum and the “Shennong Gaotangzhe”, the six tested materials of sugarcane belonged category II, and the two kinds of maize belonged category III. From the cluster diagram, the similar coefficient of “Shennong Gaotangzhe” and African sweet sorghum is the largest. It showed that the genetic distance between “Shennong Gaotangzhe” and African sweet sorghum is closer and the genetic differences is smaller than the others. The results of comparative-GISH revealed that “Shennong Gaotangzhe” shared a common ancestor with sweet sorghum, but without the descendant of sugarcane or maize. Combined with the three methods identified in this study, the “Shennong Gaotangzhe” was identified as a variety (line) of sweet sorghum, but not a hybrid of sugarcane, sorghum and maize. The results of the study not only reveal the false reports for avoiding unnecessary losses, but also explore the prospect of sweet sorghum as a germplasm resource of sugarcane for distant hybridization.