A ship-centric direct communication system and an operation method thereof are proposed. The system includes a data transmission device configured to transmit, to a data reception device through a link channel, a transmission frame composed of a plurality of slots generated according to slot time, a plurality of pilots provided for channel estimation and arranged at respective specific positions in each of the plurality of slots according to a pilot transmission period, and data symbols arranged between each of the plurality of pilots, and the data reception device configured to perform channel compensation for data present between the plurality of pilots by using the plurality of pilots for each of the plurality of slots of the transmission frame when the transmission frame is received from the data transmission device and performing linear interpolation after the channel estimation in a frequency domain, and convert channel-compensated signals back into time domain symbols.