The configurations of a bridgeless PFC circuit system and a controlling method thereof are provided. The proposed system includes a bridgeless PFC circuit having a first and a second input terminals, a first switch having a first terminal, a first inductor having a first terminal coupled to the first input terminal and a second terminal coupled to the first terminal of the first switch, and a second inductor having a first terminal coupled to the second input terminal, a first auxiliary winding coupled to the first inductor and generating a first sensing signal, and a second auxiliary winding coupled to the second inductor and generating a second sensing signal, wherein the first and the second sensing signals are used to generate an inductor current sensing signal controlling the switching of the first switch accordingly.