The invention provides a manufacturing method of an environment-friendly ecological waterproof roof. The manufacturing method of the environment-friendly ecological waterproof roof includes that basic layer repair is performed on a cast-in-situ roof, a rigid waterproof layer is built, a water and steam discharging layer is established, a water filtering layer is paved on the rigid waterproof layer, the water filtering layer is divided into zones according to intervals, water discharging grooves are arranged between the zones, semicircular blind pipes which are communicated vertically and horizontally are arranged in the water discharging grooves, the semicircular blind pipes in the water discharging grooves and roof water discharging grooves are communicated, earth for growing is paved, and earth for growing is paved on the water filtering layer. The manufacturing method of the environment-friendly ecological waterproof roof breaks a conventional thought of waterproofing work, combines prevention and drainage, gives first place to the drainage, discharges steam to reduce negative pressure by adopting two-stage water and steam discharging systems and stores water and maintains concrete under a natural state. Steam is discharged through ventilation pipes so as to reduce possibility of rotted roots of plants, a whole system is more favorable for growth of the plants, and the manufacturing method integrates functions of water storage, water discharging, steam discharging and thermal insulation and has the advantages of being low in production cost and environment-friendly in materials. Turfs, fruits and vegetables planted on the earth for growing can enhance effects of thermal insulation, sediment fixing, antifreezing, sun blocking and greening.