The on-site recovery of nucleic acid from foodborne bacteria is in high demand to further understand on-site molecular diagnosis, which is especially applicable in developing countries. Here, we first proposed a smartphone operable centrifugal system (SOCS) for nucleic acid extraction with the assistance of a low power consumable motor and hydrogel beads. The SOCS consists of a centrifugal motor, 3D-printed cartridge, a nucleic acid collection column, and a smartphone. The SOCS shows excellent DNA extraction performance within 6 min, and it can operate more than 100 times using a smartphone. The purified effluent DNA was accumulated in the nucleic acid collection column. The performance of the SOCS was confirmed by amplifying the recovered DNA from Escherichia coli O157:H7. Moreover, the artificially inoculated food and blood samples also confirmed the performance of SOCS. The proposed SOCS provides an on-site operable nucleic acid separation platform in terms of simplicity, easy usability, cost-effectiveness, and portability in pathogenic point-of-care diagnostics.