The invention provides a manufacturing method of an energy harvester based on a piezoelectric polymer micro-structure array. The manufacturing method comprises the following steps: preparing a piezoelectric polymer micro-column array on a conductive substrate and then utilizing a flat plate electrode as an upper electrode to form a pair of parallel flat plate electrodes together with the substrate; applying direct-current voltage between the electrodes; when heating the substrate until the temperature is higher than a glassy state conversion temperature of a piezoelectric polymer, carrying out flowing deformation on the micro-column array again under the induction effect of an electric field force until the micro-column array comes into contact with the upper electrode to form a large-depth-width-ratio micro-column array with a mushroom-shaped top; and in an electric field induction flowing deformation process, micro-structuralizing the piezoelectric polymer and orienting inner molecules along the direction of an electric field to obtain the energy harvester with a strong piezoelectric effect. The obtained piezoelectric polymer micro-structure array is connected with the upper and lower electrodes to directly form a finally-needed device; complicated technical control is not needed, the processing cost is greatly reduced and the working efficiency is improved.