The invention provides application of brown algae oligosaccharide or pharmaceutically acceptable salt thereof in preparation of a medicine for treating acute kidney injury, wherein the brown algae oligosaccharide is brown algae disaccharide, brown algae triose and / or brown algae tetraose. The invention also provides application of the brown algae oligosaccharide or the pharmaceutically acceptable salt thereof in preparation of medicines for preventing acute kidney injury from being converted into chronic kidney diseases. After the brown algae oligosaccharide is used for treating an animal with acute kidney injury, the serum creatinine level is obviously reduced, the urine concentration function of the kidney is obviously recovered, the levels of renal tubular injury factors (KIM-1 and NGAL) are obviously reduced, the expression of inflammatory factors is obviously reduced, the pathological change of the kidney is obviously improved, and the treatment effect is enhanced along with the increase of the dosage. Therefore, the brown algae oligosaccharide disclosed by the invention has a relatively strong effect of treating the acute kidney injury. In addition, when acute kidney injury occurs, the brown algae oligosaccharide disclosed by the invention can be used for protecting kidney functions and preventing the acute kidney injury from being converted into chronic kidney diseases.