Branched-chain keto acids (BCKAs) are derivatives from the first step in the metabolism of branched-chain amino acids (BCAAs) and can provide important information on animal health and disease. Here, a simple, reliable and effective method was developed for the determination of three BCKAs (α-ketoisocaproate, α-keto-β-methylvalerate and α-ketoisovalerate) in serum and muscle samples using high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (HPLC-Q-TOF/MS). The samples were extracted using methanol and separated on a 1.8 μm Eclipse Plus C18 column within 10 min. The mobile phase was 10 mmol L−1 ammonium acetate aqueous solution and acetonitrile. The results showed that recoveries for the three BCKAs ranged from 78.4% to 114.3% with relative standard deviation (RSD) less than 9.7%. The limit of quantitation (LOQ) were 0.06~0.23 μmol L−1 and 0.09~0.27 nmol g−1 for serum and muscle samples, respectively. The proposed method can be applied to the determination of three BCKAs in animal serum and muscle samples.