Nanometer polymer cement waterproof coating and a preparing method thereof are disclosed. The coating includes a liquid material and a powder material. The liquid material includes, by weight, 850-880 parts of an acrylate emulsion and 5-8 parts of a root blocking agent. The powder material includes, by weight, 490-505 parts of cement, and 95-105 parts of nanometer particles. The root blocking agent is poly(ethylene glycol) 2-(4-chloro-2-methylphenoxy)-propionate. The nanometer particles are nanometer silica and nanometer zeolite. Through the technical scheme, plant root puncturing resistance of the coating is improved so that the coating can be more suitable for planted roofs.