The invention provides a method collaboratively repairing soil heavy metal pollution by microorganisms, plants and biological carbon. The method specifically comprises: 1), adding a magnetotactic bacterium culture medium into heavy metal polluted soil, inoculating magnetotactic bacteria, and plowing; 2), irrigating the heavy metal polluted soil, and setting a magnetic field; 3), collecting the surface layer of the heavy metal polluted soil, and rinsing the collected heavy metal polluted soil with water; 4), planting grass family plants in the heavy metal polluted soil; 5), pulling out young ears; 6), removing the grass family plants; 7), after preparing a biological carbon mixture through processing the removed grass family plants, applying the biological carbon mixture into the heavy metal polluted soil in which the grass family plants are planted, uniformly mixing, and aging; and 8), cyclically repeating the above steps until the content of heavy metal in the soil reaches safety standards. The method is great in soil treatment effect, low in cost and high in practicability, and is safe and reliable.