A multi-chip system and a data transmission method thereof are provided. The multi-chip system includes a first chip, a link unit, and a second chip. The first chip includes multiple transmitter (TX) channels and a first data processing module. The TX channels are configured to provide at least one transaction information. The first data processing module converts the at least one transaction information into at least one first data packet according to a general packet format and packs the at least one first data packet according to a specific packet format to generate a second data packet. The first data processing module merges two sets of second data packets into a third data packet and transmits the third data packet to the link unit. The second chip receives the third data packet through the link unit.