At present, the clarinet instrument is in the process of continuous development and progress, and its range is also expanding. The intonation training in clarinet performance is a committed step in clarinet performance technology, and also the basis for achieving music performance and artistic creation. However, there are still many shortcomings in the teaching of intonation training in clarinet performance, which directly leads to the phenomenon that the teaching quality of intonation training is not high and students do not master intonation properly. This paper mainly introduces the problems of intonation training in clarinet performance, and finds that the teaching of intonation training in clarinet performance has problems such as teachers' insufficient ability to master multiple styles, teachers' and students' insufficient attention to intonation training, and inadequate control of mouth shape and breath. In clarinet performance, accurate intonation is an important reason for success. Only 2 teachers attach great importance to the intonation training in clarinet performance, accounting for only 10%. Only 5 students attach great importance to the intonation training in clarinet performance, accounting for 12.5%. It can be seen that both students and teachers attach little importance to it. On the basis of analyzing the teaching problems of intonation training in clarinet performance, this paper puts forward a targeted teaching method of intonation training. Adopting scientific methods to train clarinet intonation can help students master intonation techniques better and reach a higher level.