An in-situ purification island structure and the construction method thereof, which refers to the field of sewage treatment technology. The in-situ purification island structure comprises the upstream purification island main body and the downstream purification island main body, in which the upstream purification island main body comprises the first base backfill layer, the first lower layer, the first hydrophobic layer, the first water permeable layer and the first upper layer. The first ecological bags are set around the surface of the first base backfill layer. The first lower layer has center formed with a lower layer backfill transitional zone. The first hydrophobic layer has center formed with a hydrophobic layer backfill transitional zone. It has a good natural purifying effect on the sewage, saves the investment and cost, no limitation on the applications, the capacity and efficiency of the purifying is high, and saves the resource.