The invention provides a method for preparing a polymer micro lens array, and relates to the field of micro mechanical machining. The problems that in an existing hot press molding method, the cycle is long, cost is high, efficiency is low, and the dimensional precision and the shape of micro lenses can not be guaranteed easily are solved. The method comprises the steps that a graphical photoresist mask is formed on the surface of a silicon substrate; a microporous array is etched through a dry method; the microporous array is evenly covered with a dimethyl silicone polymer thin film, the microporous array is in sealing connection with a cavity, the pressure of a cavity is adjusted to change the ball coronary deformation of the dimethyl silicone polymer thin film, and the pressure is kept constant; photosensitive gel is poured on the dimethyl silicone polymer thin film, and a photosensitive gel convex mold is obtained through ultraviolet curing demolding; a mixture of dimethyl silicone polymer prepolymer and a curing agent is poured in the photosensitive gel convex mold to be heated and cured to obtain a dimethyl silicone polymer concave mold; the concave mold is used for conducting hot pressing on carbonic ester base materials, and a carbonic ester base micro lens array is obtained after demolding. The method for preparing the polymer micro lens array is easy to operate, high in efficiency, low in cost, small in error, good in repeatability, lossless in demolding and suitable for mass production.