An apparatus for controlling a high pressure common rail system of a diesel engine includes an operation condition parameter acquiring module configured to acquire operation condition parameters associated with the high pressure common rail system; a control quantity determining module coupled with the operation condition parameter acquiring module and configured to determine a control quantity for controlling the high-pressure common rail system based on the operation condition parameters, a target value of the fuel pressure within a high pressure common rail tube cavity and a control model designed based on a system physical model, wherein the control quantity is an equivalent cross-section area of the electromagnetic valve of a flow metering unit; and a drive signal determining module coupled to the control quantity determining module and configured to determine a drive signal for driving the flow metering unit based on the determined control quantity.