According to one embodiment of a method for interference suppression in radio-over-fiber communication systems, the method uses a mode selection module to continuously update real time information of at least two mobile stations and determine to enter a cross mode or a single mode. In the single mode, when a mobile station approaches a switching point, a single mode command is issued to control at least one first specific remote antenna unit (RAU). In the cross mode, when an immediate cross condition is a new cross condition, a new cross mode table is generated, and when the position of any one mobile station of the at least two mobile stations cross a threshold, a cross mode command is issued to control at least one second specific RAU according to a corresponding cross mode table.