Chinese golden camellias (Camellia sect. Chrysantha) are traditional substitute tea with medicinal and food properties. The development of fingerprinting techniques specific to Chinese golden camellias may provide a new means of reliably assessing the quality of tea and traditional medicine. Herein, 32 total specimens were collected in Southern China and used to establish a polyphenolic compound-based high-performance liquid chromatography (HPLC) signature profile. The established chromatographic fingerprints were subjected to similarity, hierarchical clustering analysis (HCA), together with principal component analysis (PCA) evaluations, and the uncertainty and reliability for such HPLC fingerprints were also evaluated. Similarity values for C. sect. Chrysantha samples ranged from 0.721 to 0.969 relative to the reference chromatographic fingerprint (RFP). HCA and PCA approaches were performed to classify 13 specimens of C. sect. Chrysantha from different species and regions into four categories that respectively contained 7, 1, 2, and 3 specimens. In this HPLC fingerprint, peak 11 was authenticated as rutin, while peaks 2, 4, 6, 7, 9, 12 and 13 were tentatively characterized via liquid chromatography-high-resolution mass spectrometry (LC-HRMS) as corresponding with other polyphenolic agents. Credibility analyses indicated that the macroscopic qualitative and quantitative reliability values for C. fascicularis RFP were greater than 0.9500. Taken together, statistical analyses thus confirmed that this HPLC fingerprinting strategy can be reliably used to classify and assess the quality of C. sect. Chrysantha specimens. And the qualitative and quantitative reliability analysis and systematic quantitative fingerprint methods are promising tools for future efforts to ensure the quality of C. fascicularis.