The booming Internet of Things makes smart healthcare a reality, while cloud-based medical storage systems solve the problems of large-scale storage and real-time access of medical data. The integrity of medical data outsourced in cloud-based medical storage systems has become crucial since only complete data can make a correct diagnosis, and public auditing protocol is a key technique to solve this problem. To guarantee the integrity of medical data and reduce the burden of the data owner, we propose an efficient privacy-preserving public auditing protocol for the cloud-based medical storage systems, which supports the functions of batch auditing and dynamic update of data. Detailed security analysis shows that our protocol is secure under the defined security model. In addition, we have conducted extensive performance evaluations, and the results indicate that our protocol not only remarkably reduces the computational costs of both the data owner and the third-party auditor (TPA), but also significantly improves the communication efficiency between the TPA and the cloud server. Specifically, compared with other related work, the computational cost of the TPA in our protocol is negligible and the data owner saves more than 2/3 of computational cost. In addition, as the number of challenged blocks increases, our protocol saves nearly 90% of communication overhead between the TPA and the cloud server.