The ability of liver to respond to changes in nutrient availability is essential for the maintenance of metabolic homeostasis. Autophagy is a conserved catabolic process that mobilizes intracellular nutrients to meet energy requirements in the event of nutrient deficiency. Dairy cows with severe fatty liver generally have a severe negative energy balance (NEB). Therefore, the aim of this study was to investigate the hepatic autophagy status in dairy cows with severe fatty liver. Liver and blood samples were collected from healthy (n = 15) and severe fatty liver (n = 15) cows. Liver tissue was biopsied and serum samples were collected on 3 consecutive days. Dairy cows with severe fatty liver displayed significant hepatic lipid accumulation. Activities of liver injury indicators (aspartate aminotransferase, alanine aminotransferase, glutamate dehydrogenase, and gamma-glutamyl transferase) were all greater in cows with severe fatty liver. The blood concentrations of haptoglobin and serum amyloid A were also markedly higher in dairy cows with severe fatty liver. The mRNA expression of autophagosome formation related gene ULK1 was lower in the liver of dairy cows with severe fatty liver than in healthy cows. However, the expressions of Becn1, vacuolar protein sorting 34 (Vps34), autophagy-related gene (ATG) 3, ATG5, ATG12, were comparable between these 2 groups. More importantly, the ubiquitinated proteins, protein expressions of sequestosome-1 (SQSTM1, also called p62) and microtubule-associated protein 1 light chan 3 (MAP1LC3, also called LC3)-II were significantly higher in the liver of dairy cows with severe fatty liver than in healthy cows. Moreover, transmission electron microscopy observation showed increased number of autophagosomes in the liver of dairy cows with severe fatty liver. Taken together, these results indicate that dairy cows with severe fatty liver display liver damage, systemic inflammation and impaired hepatic autophagic flux. Furthermore, impaired autophagic flux may result in liver damage and inflammation and further promote the occurrence and development of fatty liver. This study also demonstrates that the hepatic adaptive capacity is impaired in dairy cows with severe fatty liver.