The invention discloses an ecological engineering method capable of efficiently removing lipophilic trace organic substances in low-pollution water. Along the water flowing direction, a high-density microalgae pool, an aquatic plant filtering bed and a subsurface constructed wetland are arranged in sequence. A suspension algae layer is arranged in the high-density microalgae pool, an aquatic plant layer is arranged in the aquatic plant filtering bed, and the subsurface constructed wetland is divided into a subsurface constructed wetland front area and a subsurface constructed wetland rear area. The subsurface constructed wetland front area and the subsurface constructed wetland rear area are both provided with a wetland plant layer, a soil layer, a volcanic rock layer, and a coal slag layer from top to bottom. Sewage to be process is processed by going through the high-density microalgae pool, the aquatic plant filtering bed, the subsurface constructed wetland front area, and the subsurface constructed wetland rear area in sequence. The provided method integrates the technological characteristics of high-density microalgae pool, aquatic plant filtering bed and subsurface constructed wetland and prominently improves the efficiency of an ecological engineering technology on removing lipophilic trace organic substances in low-pollution water.