An oil pump system of a hybrid vehicle may include an electric oil pump which supplies operating hydraulic pressure to the transmission based on a speed command; a data detector which detects data for controlling the electric oil pump; and a controller which sets a driving mode of the electric oil pump based on the data detected by the data detector, determines a basic flow rate of the set driving mode, determines a final flow rate by compensating for the basic flow rate, and applies the speed command to the electric oil pump, in which the operating hydraulic pressure is supplied to the transmission only by the electric oil pump, and the speed command is determined based on target hydraulic pressure, an oil temperature, and the final flow rate.