A NB-IoT system and a preamble transmission method thereof are provided. The NB-IoT system includes a base station and a user equipment. The base station broadcasts a random access resource configuration. The random access resource configuration includes an NPRACH access intermitting setting. The NPRACH access intermitting setting allocates an NPRACH pause period and an NPDCCH. The user equipment receives the random access resource configuration, and transmits a preamble repeatedly in an NPRACH during a NPRACH transmission period according to the random access resource configuration. The base station detects the preamble in the NPRACH during the NPRACH transmission period, and transmits a random access feedback message in the NPDCCH during the NPRACH pause period. The user equipment receives the random access feedback message in the NPDCCH during the NPRACH pause period, and adjusts a transmission behavior of transmitting the preamble during the NPRACH transmission period.