The invention relates to a method for manufacturing a novel microfluidic chip biological fuel cell, which is characterized by comprising the following steps: 1, getting conducting glass, and removing a conducting layer in the middle of the upper surface of the conducting glass to form a left conducting layer and a right conducting layer which are mutually insulated, and a middle insulated tape; 2, processing an anode chamber groove, a nutrient solution inlet through hole, a nutrient solution outlet through hole, a cathode chamber groove, an electrolyte inlet through hole, an electrolyte outlet through hole, a salt bridge channel and a salt bridge solution inlet through hole on the lower surface of a PDMS sheet; and 3, attaching the PDMS sheet to the upper surface of the conducting glass, leading the anode chamber groove and the cathode chamber groove main body to respectively contact with the left conducting layer and the right conducting layer, injecting a hot salt bridge solution into the salt bridge solution inlet through hole, and cooling the salt bridge solution so as to be solidified into a salt bridge, wherein the salt bridge does not directly contact with the left conducting layer and the right conducting layer. The novel microfluidic control chip biological fuel cell manufactured by the method has the advantages of small size and high battery output efficiency, and can control the battery output power.