Among the basic medical sciences, anatomy and physiology (anatomy & physiology) is a fundamental subject for students majoring in nursing. Due to its diversity and difficulty, nursing students experience stress when studying it. Previous graduates generally presented lower achievements in anatomy & physiology than in other nursing‐related subjects in the National Council Licensure Examination‐Registered Nurse, indicating that anatomy & physiology education requires improvement. Accordingly, we examined the impact of innovative teaching on students' motivation and performance when learning anatomy & physiology through a quasi‐experimental pre‐/post‐test design. For innovative teaching, we used the novel interactive audio human organ model, followed by team‐based learning. The participants were 200 lower‐grade students in the nursing department of a junior college in Taiwan, divided into two groups receiving innovative teaching (experimental group) or traditional teaching (control group). Questionnaire surveys were administered, and the collected data were statistically analyzed. The innovative teaching in anatomy & physiology improved learning motivation, especially in terms of affect, executive volition, and learning performance. The essential components of learning motivation, such as value, expectation, affect, and executive volition, were positively correlated with the reaction levels of learning performance. Regarding the improvement in academic performance, the experimental group performed significantly better than the control group. The use of innovative teaching in class enhances students' learning motivation and learning performance when studying anatomy & physiology. Interactive teaching aids enhance the enjoyment of learning anatomy & physiology while facilitating in‐depth exploration of the human organs and systems.