The teaching of biological instrument analysis plays a key role in the development of modern life science field. With the deepening of life science research, new instrumental analysis techniques and methods continue to emerge. These technologies have been widely used in the fields of biology, clinical diagnosis, medicine, materials and so on with their rapidity, accuracy, good selectivity and high sensitivity. As the core component of biology teaching system, the course of biological instrument analysis is very important for cultivating students’ experimental and theoretical knowledge and scientific research ability. However, with the emergence of new testing methods and testing instruments, the course of biological instrument analysis is faced with many challenges, including lagging teaching content, single teaching method and insufficient cultivation of students’ practical ability, which directly affect the teaching effect and the improvement of students’ comprehensive quality. In view of this, this paper makes an in-depth analysis of the main problems existing in the current teaching of biological instrument analysis, and puts forward targeted improvement strategies, aiming to effectively improve the teaching effect of biological instrument analysis experiment by optimizing the course system, innovating teaching methods, strengthening practical operation and other means, and cultivate more innovative application talents with solid theoretical foundation and practical ability. In order to meet the needs of social and scientific and technological development.