The invention relates to a frequency hopping fountain code system and a transmission method thereof, in particular to a transmission method of a frequency hopping fountain code system introduced by using a novel interweaving technology, and belongs to relevant technical fields of wireless communication systems, communication signal processing, channel coding and decoding and the like. The frequency hopping fountain code system can be used for transmitting data under the condition that a part of frequency points are blocked completely under the action of interference, so that the reliability of a communication system in a severe channel environment is enhanced. A bit-interleaved coded modulation technology is adopted, so that the bit error rate performance of the system is improved. Meanwhile, the redundancy is not increased, so that the rate of information transmission is not influenced. A bit-level interleaver is adopted, and can be used for encrypting under the condition that an interleaving rule cannot be obtained by an enemy, so that the safety of information transmission is enhanced.