The invention discloses a method for removing zirconium, zinc and chromium in red mud. The method includes the steps that malic acid and acetic acid are mixed at first to be prepared into mixed organic acid, and then the mixed acid and the red mud are mixed and stirred; qualified tailings and waste liquor are obtained after filter pressing; and when heavy metal of the waste liquor is removed through recycle leaching until the pH value of the liquor is larger than 6, quick lime is added into the waste liquor for stirring, and a qualified solution can be obtained after filtering. The zirconium content in the qualified tailings is lower than 10 mg/kg, the chromium content is smaller than 5 mg/kg, the zinc content is smaller than 1 mg/kg, the residual organic acid can achieve biodegradation, harm to people, livestock and plants is avoided, and thus the qualified tailings can be used as a modifying agent for alkaline soil. The pH value of the qualified solution is 7-8.5, and the concentration of the zirconium, chromium and zinc is lower than 0.02 mg/L. The mixed organic acid is used for removing heavy metal in the red mud, and hence the method has the characteristics that chemical consumption is small, the removal rate of the heavy metal is high, the tailings can be used directly after treatment, the waste liquor can be recycled, the pH value of the waste liquor is high, the heavy metal content of the waste liquor is high and treatment and recycling of the waste liquor are easy.