A method of controlling an automotive air conditioning system includes: a mode checking step of checking whether the air conditioning system is in an auto-mode; an operation recognizing step of recognizing whether the air conditioning system is manually operated in the auto-mode; and a learning step of setting and storing at least one manual operation value, when the air conditioning system is manually operated, and then operating the air conditioning system in accordance with the at least one stored manual operation value in a next auto-mode.