The invention relates to a roof ecological planting system and a construction method thereof. An insulating layer, a waterproof anti-root piercing layer, a cement mortar protective layer, a drainage layer, a filtering layer, a plant substrate layer and a roof utilization layer are arranged on a base structure layer sequentially, wherein the waterproof anti-root piercing layer adopts an anti-plantroot piercing waterproof coating; the drainage layer adopts plastic anti-drainage plates; and joints between the plastic anti-drainage plates and the periphery of a pipeline are bonded by an anti-plant root piercing adhesive. The entire system has the advantages of reducing construction processes, shortening construction period and lowering construction cost, along with excellent material performance and clear function of each layer. Three anti-plant root piercing protection lines consist of the anti-plant root piercing waterproof coating, a drainage plate, a cement mortar protective layer and the anti-plant root piercing adhesive, so that the system can adapt to normal growth of various plants and the waterproof function of a roof for long-term use is guaranteed.