A method of transporting data with embedded clock including following steps is provided. In an initial stage, a first bit length and a second bit length are determined. Original data is received. The original data is packed with every N bits as a packet, where N is at least 4. It is analyzed whether a long-run length of long-run data with consecutive same bit data in the packet is greater than N/2. The packet is coded to embed clock/toggle information with the first bit length into the packet. The clock/toggle information determines whether the long-run data is toggled. An appearance frequency of the clock/toggle information is clock information. If the long-run length is not greater than N/2, the long-run data is not toggled. If the long-run length is greater than N/2, bit with the second bit length after an Lth bit of the long-run data is toggled.