The invention discloses a three-dimensional flexible neural microelectrode and a manufacturing method thereof. The microelectrode uses a flexible polymer as a base material, and performs progressive electroplating through a circular pattern design of a metal seed layer to form smooth three-dimensional convex features. The electrode site structure can not only ensure good contact between the electrode site and the nerve cells, but also avoid damage to the nerve tissue caused by the sharp edges and corners of the raised electrode sites in the existing three-dimensional neural microelectrode. In addition, through the composite electroplating process in the electroplating process, that is, nano-scale dispersants are added to the electroplating solution to form a submicron-scale microporous structure on the surface of the electrode, increasing the surface area of the electrode site, thereby enhancing the current output capability of the electrode and ensuring the nerve. Effective stimulation of microelectrodes under the constraints of biosafety conditions. The three-dimensional flexible neural microelectrode provided by the invention can be widely used in the fields of neurological disease treatment, neurological rehabilitation, neurobiological basic research and the like.