Provided are a digital communication system using frequency selective baseband and a method thereof. A transmitter of the digital communication system, includes: a preamble/header transmission processing unit for spreading a preamble for frame synchronization and a header including data information; a data transmission processing unit for spreading data by using spread codes having dominant frequency in a desired frequency band, i.e., frequency selective spread codes; and a multiplexer for multiplexing the spreaded preamble and the spreaded header from the preamble/header transmission processing unit and the frequency selective spreaded data from the data transmission processing unit and transmitting the multiplexed signal in digital.