The invention provides a microbiological fuel cell for synchronously restoring organic matters and heavy metals in polluted bottom mud. The microbiological fuel cell comprises an anode, a cathode and an external resistor conductively connected with the anode and the cathode, wherein the anode is buried in the polluted bottom mud; the cathode is a mesh electrode fixed on water and serves as a carrier for supporting growth of an aquatic plant; the external resistor comprises an overwater part of the aquatic plant; and the polluted bottom mud is in an anaerobic environment. The invention further provides a method of synchronously restoring the organic matters and the heavy metals in the polluted bottom mud. Anaerobic microorganisms at the anode and the aquatic plant at the cathode have a synergistic effect on organic matter degradation and heavy metal removal in the bottom mud; the heavy metal and organic matter pollution in the bottom mud can be alleviated at the same time; chemical energy of the organic matters in the bottom mud is converted into electric energy and used for pollution reduction; a dissolution-balancing effect of the heavy metals and the organic matters between the bottom mud and a water body can be reduced; a win-win concept of environmental protection and pollutant recycling is sufficiently embodied.