LED controllers, LED lighting systems and control methods capable of providing an average luminance intensity independent from the variation of an AC voltage. LEDs are divided into LED groups electrically connected in series between a power source and a ground. A disclosed LED controller has path switches, a management center and a line waveform sensor. Each path switch is for coupling a corresponding LED group to the ground. The management center controls the path switches. When turning off an upstream path switch, the management center controls a downstream path switch for a downstream LED group to make the driving current passing the upstream LED group substantially approach a target value. The line waveform sensor is coupled to the power source, sensing the waveform of the input voltage of the power source. The line waveform sensor is configured to decrease the target value when the input voltage increases.