Anatomy practical classes are an essential part of learning human anatomy. The flipped classroom teaching model has been used in medical education in recent years. However, its precise impacts on anatomical knowledge acquisition and learning outcomes remain controversial. With the development of information technology, new educational tools, such as Rain Classroom, have recently attracted much interest. The Rain Classroom is an application that can easily connect students and teachers through smartphones or computers. However, whether and how to apply it to the flipped classroom in anatomy practical classes needs to be evaluated. In this study, we designed a teaching model of flipped classroom assisted by Rain Classroom and carried it out in anatomy practical classes at our university. Results showed that the final exam scores of the experimental group were significantly improved, compared with the control group (p < 0.01); the final exam score was significantly correlated with both the pre-class quiz score (p < 0.05) and the in-class quiz score (p < 0.001). Student satisfaction was measured by a questionnaire on a Likert scale of 1-5. All the mean scores were greater than 4.5, indicating that most students had positive attitudes toward this teaching model. The present study suggests that the Rain Classroom helps support students throughout the learning processes of the flipped classroom, and the model of flipped classroom assisted by Rain Classroom could improve students' learning efficiency and ultimately increase their exam performance in anatomy practical classes.