Polyamines and their N-acetylated metabolites are potential biomarkers in the diagnosis and therapeutic evaluation of cancer. Thus, we present here an ultra high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method for the simultaneous determination of 6 free, 3 monoacetylated, and 2 diacetylated polyamines without derivatization. The major improvement of this method is the use of 0.2 % perfluoroheptanoic acid methanol in the pretreatment step to achieve protein precipitation and 0.0125 % perfluoroheptanoic acid in the mobile phase to achieve analyte separation within 9 min. The established analytical method was validated with plasma, urine, and liver tissue and applied to determine plasma, urine, and liver tissue samples from healthy rats, hepatocellular carcinoma rats, and administrated rats successfully. Results indicated free polyamines such as putrescine mainly existed in liver tissue but more polar N-acetylated metabolites such as N (1),N (12)-diacetylspermine seemed to exist in biological fluid. After carcinogenesis, the levels of polyamines were increased, but the elevated levels of polyamines and their metabolites tended to decrease when administrated with anticancer drug. The method provided a more versatile manner for clinical application in the diagnosis and therapeutic evaluation of hepatocellular carcinoma.