A method for transforming a data stream and a communication system thereof are provided. In a second communication terminal, a padding data of the data stream of a first communication terminal is checked whether it corresponds to a default value so as to determine whether a first bit order used for the data stream of the first communication terminal is consistent with a second bit order used for a data stream of the second communication terminal. When the padding data does not correspond to the default value, the data stream transmitted from the first communication terminal is transformed from the first bit order to the second bit order by the second communication terminal.