A method for controlling an engine variable valve timing of a hybrid electric vehicle, may include providing a cam position setting table of a fuel efficiency prioritized intake/exhaust cam control mode, and a cam position setting table of a normal intake/exhaust cam control mode, the cam position setting table of the fuel efficiency prioritized intake/exhaust cam control mode being differentiated from the cam position setting table of the normal intake/exhaust cam control mode; selecting one of the fuel efficiency prioritized intake/exhaust cam control mode and the normal intake/exhaust cam control mode by a canister loading amount and whether or not diagnosis of an intake cam and diagnosis of an exhaust cam are completed; and determining position control values of the intake and exhaust cams by using the cam position setting table and then controlling positions of the intake cam and the exhaust cam by the determined position control values.