The Belle II experiment and the SuperKEKB collider are designed to operate under a higher luminosity compared to that of Belle for the improvement of rare $B$ meson decay study and new physics search. To break the bottleneck of bandwidth and to improve the stability in the operation of the Belle II data acquisition (DAQ) system, a new PCI-express-based readout system has been developed. The new system includes a PCI-express-based high-speed readout board (PCIe40), which was originally developed for the upgrades of the LHCb and ALICE experiments, the PCIe40 firmware, the slow control, and readout software running on a readout PC. The new readout system’s commissioning with most of the Belle II subdetectors has been performed, and the readout upgrade is complete for the particle-identification detectors and the neutral kaon and muon detector in Belle II, which has been operating stably with the new system in the beam collision “physics runs.” The results of the commissioning and the performance of the global DAQ operation will be reported.