The invention provides a method for preparing biodiesel from grease of livestock and poultry dying from non-virulent diseases. The method includes the steps of firstly, pretreating the grease of the livestock and poultry which die from diseases so as to obtain raw oil, wherein the pretreating method includes decoloring, deodorizing, degumming, standing to remove impurities, washing with water, discharging water and drying; secondly, subjecting the raw oil to pre-esterification reaction, namely enabling methyl alcohol and the raw oil to react in a three-dimensional ultrasonic reactor with concentrated sulfuric acid as a catalyst so as to obtain low-acid-value grease; thirdly, subjecting the low-acid-value grease to esterification reaction, namely subjecting the methanol and the low-acid-value grease to esterification reaction in an oscillator with potassium hydroxide as a catalyst, taking out the esterified product according to a specified reaction time, taking an upper biodiesel phase,washing with water and carrying out reduced-pressure distillation. The method provides a new idea for enriching the source of raw oil of the biodiesel and realizing harmless treatment of the livestock and poultry dying from the diseases and industrialized production of the biodiesel.