Flexible neural microelectrodes demonstrate higher compliance and better biocompatibility than rigid electrodes. They have multiple microfilaments can be freely distributed across different brain regions. However, high-density fan-out of high-throughput flexible microelectrodes remains a challenge since monolithic integration between electrodes and circuits is not currently available as it is for silicon electrodes. Here, we proposed a high-density fan-out strategy for high-throughput flexible electrodes. The flexible electrodes are partially overlapped on the printed circuit board (PCB). A modified wire bonding method is used to reduce the pads area on the PCB. Both the traces and pads on the PCB are optimized to minimize the back-end package. It is significantly reducing the connection area. In addition, the vertical rather than horizontal connection between the connector and the PCB further decrease the volume of the package. 1024 channel flexible electrodes are bonded to the high-density PCB within an area of 11.8*10mm2, and the success connection rate can reach 100%. The high-density fan-out strategy proposed in this paper can effectively reduce the volume of high-throughput flexible electrodes after packaging, which facilitates the miniaturization of in vivo multichannel recording devices and contributes to long-term recording.