A host controller with suppressed data jitter is shown, which uses a logical physical layer (LPHY) to provide groups of low-speed data, uses a clock-domain-crossing transmitter (TXCDC) to transmit the groups of the low-speed data to the corresponding electrical physical layers (EPHYs), uses the EPHYs to convert the groups of the low-speed data to high-speed data and transmit the high-speed data to the corresponding external devices, and further has a multiplexer. Each EPHY corresponds to one clock signal and operates accordingly. The multiplexer receives the clock signals of the EPHYs to output a common clock signal for the LPHY to provide the groups of low-speed data and for the TXCDC to retrieve the groups of low-speed data. With respect to each of the external devices, the TXCDC uses the clock signal corresponding to the corresponding EPHY to output the corresponding group of low-speed data to the corresponding EPHY.