As a traditional musical instrument, the flute has a long history and is loved by people. The flute has a wider range, and its timbre has strong penetrating and expressive power. This is not only a unique solo instrument but also occupies an important position in the symphony orchestra. Breath training on the flute is an essential step in flute learning. However, in the traditional flute breath training process, teachers cannot observe the students’ practice in real time, and the training process is relatively simple, resulting in the final training effect not being obvious and the students’ breath stability not being significantly improved. In order to solve this problem, this paper applied the Internet of Things (IoT) big data technology to the flute breath training process. The flute breath training system based on big data of Internet of Things was used to conduct professional breath training for students. Through the tests of the trained students, it was found that the training method of flute breath using the big data of the Internet of Things improved the students’ leg strength and chest, abdomen, and back strength. In the long-tone practice, the students’ exhalation time increased by 1.472 seconds, and the students’ breath stability increased by 7.1%, which laid a good foundation for the students to learn the flute in the future.