Provided is a cylinder intake air amount estimation apparatus for an internal combustion engine, which is capable of highly precisely calculating a cylinder intake air amount based on an AFS intake air amount in a control system for an engine including a supercharger. A cylinder intake air amount calculation part calculates the cylinder intake air amount based on an intake opening intake air amount by using a physical model of an intake system derived based on a volume efficiency acquired by considering an intake manifold as a reference, which is a volume efficiency of air entering a cylinder from the intake manifold, a virtual intake manifold volume, and a stroke volume per cylinder, the physical model being adapted to the control system for an engine including a supercharger.