Evodiae Fructus (EF) is generally divided into three categories: small flower EF (SEF), medium flower EF (MEF) and big flower EF (BEF) in commodity circulation according to the size of the fruit. It is a well-known and frequently used herbal medicine for treating gastrointestinal disorder-related stomachache and headache, which has aroused wide attention for its hepatotoxicity. However, reports about hepatotoxicity is controversial and hepatotoxic components are inconclusive. The study aimed to explain the controversial hepatotoxicity of EF and screen the components associated with hepatotoxicity of EF based on the spectrum-toxicity relationship. UPLC fingerprints of 39 batches of EF collected from different regions were established. Combined with the results of L02 cell viability assays, the spectrum-toxicity relationship was investigated on the basic of orthogonal partial least squares (OPLS). The results of the research demonstrated that the toxicity of EF was obviously various among the different categories, in particularly, SEF was with less toxicity, MEF except for adulterants and BEF had mild toxicity and adulterants of MEF (A-MEF) produced more damage to L02 cell and no regions specificity in hepatotoxicity of EF. Thereinto, samples, the contents of which do not meet the requirements of Chinese Pharmacopoeia, were adulterants. It was worth noting that P11, P17, P20 and P25 were closely related to hepatotoxicity of EF and they were respectively identified as limonin (LIM), evodiamine (EVO), 1-methyl-2-nonyl-4(1H)-quinolone (MNQ), and 1-methyl-2-undecyl-4(1H)-quinolone (MUQ) by UPLC-Q-Exactive-MS. The hepatoprotection of P11 and hepatotoxicity of P17 were consistent with the results of spectrum-toxicity relationship. In summary, A-MEF was more toxic than other categories and SEF was less toxic than the others. It was noteworthy that EVO was the main hepatotoxic component of EF and LIM was the main hepatoprotective component of EF. The results provided worthy evidence for better utilization and development of EF.