An intelligent GUI touch control method and system, the method includes the steps of: generating at least one masking plane according to a GUI, wherein the GUI includes at least one option object, the masking plane has at least one masking block corresponding to the at least one option object, the masking block has a plurality of sub-blocks, and each of the sub-blocks has a weighting coefficient; reading a sensed data array from a touch panel; and performing a weighting operation according to the at least one masking plane and the sensed data array, so as to make each of the at least one option object correspond to at least one weighted value, and determine at least one target object among the at least one option object according to the at least one weighted value.