A medical device diagnostic apparatus and a control method thereof are provided. The medical device diagnostic apparatus includes a communicator connected to a controlled medical device, the communicator being configured to transmit and receive data to and from the controlled medical device, and a controller configured to select a component from components of the controlled medical device based on the received data, calculate a difference value between input and output data of the selected component and input and output data corresponding to the selected component in reference data, determine whether the difference value is greater than a value, determine that the selected component operates abnormally in response to the controller determining that difference value is greater than the value, and select another component from the components in response to the controller determining that the difference value is less than or equal to the value.