A method for controlling an engine of a vehicle includes: monitoring, by a controller, engine operation data including a crank position and an engine rotation speed; obtaining, by the controller, a measured air amount flowing into to a specific cylinder; calculating, by the controller, an expected air amount at an intake valve closing time based on the measured air amount; calculating, by the controller, a fuel amount based on the expected air amount; calculating, by the controller, an ignition timing based on the engine rotation speed and the expected air amount; and injecting, by the controller, the calculated fuel amount and performing ignition at the ignition timing.