The invention discloses a composite modifying agent for restoring farmland polluted soil and a preparation method of the composite modifying agent and relates to the field of modern agriculture. The problem that in an existing polluted soil restoring method, dual restoration functions of soil polluted heavy metal and organic matter cannot be achieved is solved. The composite modifying agent comprises, by weight, 3-9 parts of a composite microbial agent, 40-60 parts of peat soil, 30-50 parts of straw powder, 3-5 parts of cake powder, 0.1-0.3 part of quick lime, 0.2-0.4 part of dipotassium phosphate, 0.5-1.5 parts of ammonium sulfate, 20-40 parts of diatomite, 20-40 parts of humic acid, 20-40 parts of zeolite, 5-15 parts of active carbon, 1-3 parts of sepiolite and 1-3 parts of chitosan. The composite modifying agent can effectively remove heavy metal in the soil and degrade organic pollutants in the soil, has dual restoration functions, cannot cause secondary pollution and can increase the crop yield; and cost is low, the restoration time is short, preparation is easy and convenient, and the restoration effect is good.