Epimedium has a long history as a traditional Chinese medicine (TCM) and is widely used. With similar morphology, non-official species, some of which have a low efficacy or even side effects, are adulterated into official Epimedium. Quality control of Epimedium is vital to its medical use. In this paper, the unitary and binary chromatographic fingerprints of 48 Epimedium samples were developed on two complementary platforms of high performance liquid chromatography-diode array detector (HPLC-DAD) and gas chromatography-mass spectrometry (GC-MS), by which complex volatile and non-volatile compounds from Epimedium were analyzed and well validated, respectively. Subsequently, principal component analysis (PCA) was performed with the unitary and binary chromatographic fingerprints of the whole chromatographic profile and common peaks. By comparison, the HPLC-DAD fingerprints alone showed a complete separation of all species, while GC-MS just provided a classification for them. Meanwhile, the fused data matrix possessed consistent classification results with HPLC-DAD analysis. Moreover, as a complementary method for conventional unitary HPLC fingerprinting, we proposed the whole fused fingerprints with several characteristic peaks, including peak 34 (n-hexadecanoic acid), 10 (icariin), 8 (epimedin C), 32 (tetradecanoic acid), 7 (epimedin B), 13, 35 (9-octadecenoic acid), 6 (epimedin A) and 11 for the quality control of Epimedium. The proposed method can provide a more comprehensive and objective quality control for Epimedium and other TCMs, and offer the feasibility for characterization and quality control of complex samples in the same genus designated under a single herbal drug entity.