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The essential oil from Curcumae wenyujin (CWEO) has antibacterial activity, but the antibacterial compounds in the CWEO have not been identified. The spectrum-effect relationship between chemical compositions and pharmacological activity is regarded as a potentially useful tool to screen bioactive compounds. The binary chromatographic fingerprint of CWEO was established by gas chromatography/mass spectrometry (GC-MS) and high-performance liquid chromatography/diode-array (HPLC-DAD). A data-level information integration method was used to investigate the chemical characteristics encoded in two chromatographic fingerprints. Additionally, the antibacterial activity against Escherichia coli (E. coli）was determined by the liquid dilution method. The spectrum-effect relationship between the binary chromatographic fingerprint and antibacterial activity was investigated with principal component analysis (PCA) and orthogonal projection to latent structures (OPLS) analysis. Compared with a single data matrix, the combined data matrix allowed more accurate identification of the strong outliers in the PCA. Additionally, the results of OPLS were used to establish a spectrum-effect relationship with a closer correlation than that generated with the single data matrix. The results indicated that germacrone, curdione, and furanodiene were detected in HPLC and GC-MS fingerprints, and may be the main antibacterial components. Abbreviations: CWEO, essential oil from C. wenyujin; MIC, minimum inhibitory concentration; OPLS, orthogonal projection to latent structures.