The Internet of Things (IoT) plays a crucial role in the generation of new, intelligent information technologies. Generally, the IoT facilities are composed of lightweight devices, and they expand computing and storage resources primarily through the cloud. Massive data collected by intelligent devices will be stored in cloud servers, but the vulnerabilities of cloud servers will directly threaten the security and reliability of the IoT. To ensure the integrity of data in the cloud, data owners need to audit the integrity of their outsourced data. Recently, several remote data integrity batch auditing protocols have been proposed to reduce transmission loss and time cost in the auditing process. However, most of them cannot resist collusion attacks. Meanwhile, certificate management problem exists in their system, which brings an enormous burden on the system. In this paper, we construct a certificate-based remote data integrity batch auditing protocol which can issue batch auditing and resist the highest level of collusion attacks—the fully chosen-key attacks for cloud-IoT . Our protocol makes use of a certificate-based cryptosystem which gets rid of the certificate management problem and key escrow problem, with no need for secret channels. Our protocol is proved to be secure in the random oracle model and implemented to show its efficiency. The simulation results illustrate that, in the case of enhanced security, our batch auditing protocol still has computational efficiency and practicability.