The invention belongs to the technical field of microfluidic control and particularly discloses a nanoneedle-electrode-based flexible microfluidic control device. The device comprises a nanoneedle sensor and a cell culture vessel which is made of a PDMS module and provided with a through hole in the middle; the nanoneedle sensor comprises a hollow gold nanoneedle electrode array, a serpentine flexible lead and a counter electrode, and the hollow gold nanoneedle electrode array is encapsulated through an insulating layer and disposed at the bottom of the cell culture vessel and partially corresponds to the position of the through hole; one side of the gold nanoneedle faces upward and is partially exposed from the bottom of the through hole. The microfluidic control device has great biocompatibility and expands the thinking for the selection of nerve electrode materials; meanwhile, the hollow gold nanoneedle electrode array has a large surface area, high density and small size and can realize stable nerve recording with a high signal-to-noise ratio. The device can adapt to biological tissue, has good biocompatibility, is suitable for implantation in vivo and has a good application prospect. In addition, the device can simultaneously realize intracellular recording, high-throughput parallel recording and in-vivo tissue recording.