Constructing selfing populations is one of the important pathways for breeding new cassava varieties. To investigate the genetic differences within the selfing populations of the edible cassava variety ‘Gui 11’ and to screen for superior germplasm, ‘Gui 11’ selfing populations were carried out through a phenotypic identification and genetic diversity analysis. These analyses included phenotypic trait evaluation, variation coefficient, genetic diversity index, correlation and principal component analysis, SSR polymorphism ratios, genetic similarity coefficients, and cluster analysis. The results indicated that the 99 resources of the edible cassava variety ‘Gui 11’ selfing populations exhibited differences in 43 phenotypic traits. The variation coefficient for 33 qualitative traits ranged from 7.14% to 994.99%, with the highest in fruit and the lowest in petiole growth oriention. The genetic diversity index ranged from 0.06 to 1.59, with the highest in branching level and the lowest in petiole growth oriention. The coefficient of variation for 10 quantitative traits ranged from 13.49% to 62.30%, with the highest in branching height and the lowest in internode spacing; the genetic diversity index for 10 quantitative traits ranged from 1.78 to 2.09, with the highest in lobed leaf length and the lowest in plant height. A total of 15 principal components were extracted from the 43 phenotypic traits, with 27 phenotypic traits such as the color of the main stem inner bark, young stem color, vein color, and top leaf color, which can be used as the main indicators for the identification of this selfing population. Genetic diversity analysis using SSR molecular markers revealed that 25 pairs of primers amplified 148 bands, with a polymorphism ratio of 83.56%. The genetic variation among the resources of ‘Gui 11’ selfing populations was substantial, with genetic similarity coefficients ranging from 0.48 to 0.91. The highest genetic similarity coefficient was between line 94 and the parent ‘Gui 11’ at 0.78, and the lowest was between line 143 and the parent at 0.59. In this study, a batch of specific germplasm and intermediate materials have been selected through the identification and evaluation of the population, which enriched the genetic diversity of cassava germplasm resources in China and provided a research foundation for the breeding of new edible cassava varieties.