Coreopsis tinctoria Nutt. is an important ethnomedicine traditionally used in Xinjiang, China. This study employed ITS2 barcode sequencing for species authentication of commercial C. tinctoria samples. Furthermore, a comprehensive quality evaluation system was established based on HPLC fingerprinting, quantitative analysis of multiple markers, and chemical pattern recognition. A total of 35 batches of C. tinctoria samples were collected from different growing regions in Xinjiang. Genomic DNA was extracted from leaves, and the ITS2 region was amplified by PCR followed by sequencing. The obtained sequences were assembled, proofread, and validated through BLAST analysis against the NCBI database. Subsequently, a neighbor-joining (NJ) phylogenetic tree was constructed based on the aligned sequences. Chromatographic fingerprinting was performed on a ZORBAX SB-C18 column (250 mm × 4.6 mm, 5 μm). Similarity analysis of the full-spectrum fingerprints was conducted using the "Similarity Evaluation System for Chromatographic Fingerprint of Traditional Chinese Medicine (2012 version)". Chemometric approaches including cluster analysis (CA), principal component analysis (PCA), and partial least squares-discriminant analysis (PLS-DA) were employed. Furthermore, a validated HPLC method was developed for simultaneous quantification of four characteristic constituents. The results showed that the main haplotypes of ITS2 sequences in 35 C. tinctoria samples were H1/H2, with a length of 225 bp. The intraspecific variation was small, and the sequences were relatively conservative, indicating that ITS2 sequences can be used as a reliable DNA barcode for the identification of C. tinctoria. The HPLC fingerprinting showed 16 common peaks, and chlorogenic acid, flavanomarein, marein, and isochlorogenic acid A were successfully identified. The similarity of the samples ranged from 0.936 to 0.998. CA classified the samples into three groups, PCA obtained five principal components with a cumulative variance contribution rate of 84.953%, and PLS-DA identified eight components, including chlorogenic acid, flavanomarein, marein, as markers for regional differences. Quantitative analysis showed that the mass fractions of the four components were as follows: Chlorogenic acid 0.860-7.504 mg·g^-1, flavanomarein 3.368-19.182 mg·g^-1, marein 19.719-83.492 mg·g^-1, and isochlorogenic acid A 2.039-12.568 mg·g^-1. The DNA barcoding technique and integrated HPLC fingerprinting/multi-component method demonstrated high reliability and stability. This study provides a scientific foundation for quality control and further research on C. tinctoria.