SuperKEKB has two main rings (MRs), namely low- and high-energy rings, with circumferences of 3 km; beam transport (BT) lines; and a positron damping ring (PDR). We upgraded the MRs and BT line vacuum control systems and designed a new PDR vacuum control system for upgrading KEKB to SuperKEKB.Here, we describe the basic configuration of the vacuum control system, which includes the interlock logic (gate valve open/closed control, non-evaporable getter pump activation, and beam abortion). We subsequently present the collimator driving system and the cooling water control system for the beam pipe of the final focusing superconducting quadrupole magnet as examples of special SuperKEKB vacuum control systems. Examples of problems in the SuperKEKB vacuum control system, including the discharge at the high-voltage connector of the ion pump, stoppage of the cooling water pump for the vacuum system, and failure of the collimator position measurement device are described.