An update control system and method of a vehicle controller are capable of determining whether a user's vehicle is being updated, based on a state-of-charge (SOC) change rate pattern indicating a degree of SOC change reduced while other vehicles are performing the corresponding update upon determining whether to perform an update using an OTA service. The system and the method re-extract a SOC change rate pattern by using a change in a SOC value measured at the beginning of an update in the corresponding vehicle to re-calculate a remaining SOC value. Thus, the success rate of a controller update using the OTA service and the update performance rate in which an actual update is in progress are increased.