Sect. Tuberculate Chang belongs to the genus Camellia, which is an endemic group in China and has high research value. However, the phenotypic patterns of this taxon are complex and diverse, and the phenotypic variation in key traits is still unclear. In this study, a total of 212 samples from 18 populations of sect. Tuberculate plants were studied for 30 phenotypic traits of flowers, fruits, and leaves using analysis of variance, correlation analysis, principal component analysis, and cluster analysis. The results showed the following. (1) The plants in sect. Tuberculate were rich in phenotypic trait variation and possessed rich phenotypic diversity. The differentiation of phenotypic traits mainly came from among populations, with leaves (66.804%) being the largest and flowers (53.476%) being the smallest. Qualitative traits (70.264%) were greater than quantitative traits (57.608%). (2) Correlation analyses showed close and complex relationships among the phenotypic traits of flowers, fruits, and leaves. (3) The cumulative contribution of the first 10 principal components was up to 73.49%, which screened out 12 major traits contributing to the phenotypic differences in plants of sect. Tuberculate. (4) Q-type analysis showed that they were classified into 18 taxa at a Euclidean distance of 7.5 and 11 taxa at a Euclidean distance of 10. The 18 populations were not fully clustered according to the geographic distance of the plants, and there was an overlap between some of the populations. In summary, the degree of variation in phenotypic traits among populations of sect. Tuberculate plants is high, which is affected by the climatic environment. The 12 major phenotypic traits screened can be used as the basis for the classification of sect. Tuberculate plants. There are trait overlaps among some populations, which may be affected by the stochastic influence of the geographic climate and gene flow. This study will provide important references for interspecific identification, classification system construction, genetic mechanism, germplasm resource conservation, and exploitation of plants in sect. Tuberculate.