The present invention provides an image reading system and an image reading apparatus with which an environment for performing a specific scan mode can be constructed with ease according to the functions of connected information processing apparatuses and the scan environment can be changed with ease, and control methods and programs thereof. To accomplish this, the image reading apparatus selects an information processing apparatus to which image data read from an original is to be transmitted, transmits identification information for identifying the image reading apparatus stored in advance in a memory and an instruction to construct an environment for performing the specific scan mode to the selected information processing apparatus, receives a response to the transmitted instruction, and, when the response is received, displays a setting screen in which settings regarding the environment for performing the specific scan mode can be changed on a display.