The invention discloses an iron humate-microbe composite soil pollution repairing agent and a preparation method thereof. The composite repairing agent is composed of iron humate and humus reducing bacterium, wherein the humus reducing bacterium is shewanella putrefaciens or South Korea comamonas; each millimeter of composite repairing agent comprises 0.002 to 0.01 gram of iron humate, the number of humus reducing bacterium in each millimeter of composite repairing agent is more than 10<8>CFU; the iron humate is a complex prepared from humic acid and Fe(SO4).7H2O; the preparation method of the composite repairing agent comprises the following steps: extracting humic acid, preparing iron humate, culturing bacterium strains in a shake flask, carrying out fermentation to prepare inoculant, and mixing to prepare the repairing agent. Compared with the prior art, the provided repairing agent can be used to repair soil polluted by organic compounds, and has the advantages of good repairing effect, quick repairing speed, low production cost, simple and convenient preparation method, and easiness for large scale production.