The invention provides a method for remediating heavy metal-organic matter composite contaminated soil. The method sequentially comprises the steps of building a leaching slope, paving the soil, carrying out heterogeneous physical and chemical leaching, backfilling, carrying out in-situ biodegradation and carrying out phytoremediation. According to the method, contaminants in the soil can be rapidly and effectively degraded, the remediation period of the contaminated soil is shortened, the remediation cost is low, no secondary contamination is caused, the method is simple and feasible, the fertility of the soil in contaminated sites can be improved, and the method is suitable for remediating the contaminated sites with various scale. The method can be used for remediating the soil contaminated by heavy metal such as Mn, Pb, As and Cu and the soil compositely contaminated by the organic matter such as petroleum and polycyclic aromatic hydrocarbon.