In the upgrade from the KEKB B-factory (KEKB) to the SuperKEKB, approximately 90% and 20% of the beam pipes and vacuum components of the positron ring and the electron ring, respectively, were replaced with new ones. In the Phase-1 commissioning in 2016, vacuum scrubbing and confirmation of the stabilities of new vacuum components at approximately 1 A were carried out, and some problems, such as pressure bursts accompanied with beam losses, were revealed. During the subsequent shutdown, the countermeasures against the problems were taken, and new beam pipes and components, such as beam pipes for the interaction point, and beam collimators were installed. The Phase-2 commissioning, where beam collision tuning was mainly performed, was carried out from March to July 2018. The collimators suppressed the background noise of the particle detector for high-energy physics (Belle II detector) very well, and the frequency of the pressure burst drastically decreased though typical beam currents were lower than those in Phase-1. So far, the vacuum system of the SuperKEKB has been working generally well, and no serious problems have been observed.