The Belle II experiment is a new generation B-factory experiment at KEK in Japan aiming at the search for New Physics in a huge sample of B-meson decays. The commissioning of the accelerator and the detector for the first physics run has started from March this year. The Belle II High Level Trigger (HLT) is fully working in the beam run. The HLT is now operated with 1600 cores clusterized in 5 units, which is 1/4 of the full configuration. The software trigger is performed using the same oﬄine reconstruction code, and events are classified into a set of physics categories. Only the events in the categories of interest are finally sent out to the storage. Live data quality monitoring is also performed on HLT. For the selected events, the reconstructed tracks are extrapolated to the surface of the pixel detector (PXD) and quickly fed back to the readout electronics for the real time data reduction by sending only the associated hits. The maximum trigger rate in the first physics run was 3.5kHz, and the Belle II data acquisition system was stably operated. There were several problems in the HLT operation, but they have successfully been fixed during the data taking period. The HLT reduction factor is measured to be 8 which is still higher than the design because of the high background environment.