The present disclosure relates to an apparatus for controlling the parking of a vehicle, a system having the same, and a method thereof. the apparatus for controlling parking of a vehicle includes a processor determining whether to generate a virtual object, depending on a length of a parking space and a current location of a vehicle, determining a parking target space in the parking space based on the virtual object upon generating the virtual object, generating a parking trajectory such that the vehicle is parked to the parking target space, to perform parking control based on the parking trajectory, when the parking space between a first object and a second object is scanned, and storage storing information generated by the processor.