Abstract: A clock multiplexer device, a controller and a storage device are provided. The clock multiplexer device comprises a clock switching timing controller and a clock multiplexer. The clock switching timing controller is configured to receive and operate at a reference clock signal being active and generate a clock switching trigger signal according to a plurality of clock signals, wherein the reference clock signal is independent of the plurality of clock signals. The clock multiplexer is for receiving the clock switching trigger signal and the plurality of clock signals, and selects one of the plurality of clock signals according to the clock switching trigger signal so as to output a target clock signal.