Abstract: Disclosed herein is a method of preparing biodiesel, including the steps of: removing foreign materials from biodiesel raw oil containing lower fatty acid and having an acid value of 20 mgKOH/g or less with an adsorbent; dewatering the foreign materials removed biodiesel raw oil; passing the dewatered biodiesel raw oil through a solid acid catalyst reaction guard bed provided with a cation exchange resin for removing metal cations at 20˜80° C. at a flow rate of 6 vol % (6 SV) or less, mixing methanol with the passed biodiesel raw oil, and then passing the mixture through a solid acid catalyst reaction main bed provided with a solid acid catalyst for an esterification reaction at 70˜120° C. at a flow rate of 0.5˜1.5 SV to adjust a final acid value of the biodiesel raw oil to 5 mgKOH/g or less; and reacting the biodiesel raw oil having the final acid value of 5 mgKOH/g or less in the presence of an alkali catalyst.