Within the framework of 6G networks, the rapid proliferation of Internet of Things (IoT) devices, coupled with their decentralized and heterogeneous characteristics, presents substantial security challenges. Conventional centralized systems face significant challenges in effectively managing the diverse range of IoT devices, and they are inadequate in addressing the requirements for reduced latency and the efficient processing and analysis of large-scale data. To tackle these challenges, this paper introduces a zero-trust access control framework that integrates blockchain technology with inner-product encryption. By using smart contracts for automated access control, a reputation-based trust model for decentralized identity management, and inner-product encryption for fine-grained access control, the framework ensures data security and efficiency. Firstly, smart contracts are employed to automate access control, and software-defined boundaries are defined for different application domains. Secondly, through a trust model based on a consensus algorithm of node reputation values and a registration-based inner-product encryption algorithm supporting fine-grained access control, zero-trust self-sovereign enhanced identity management in the 6G environment of the Internet of Things is achieved. Furthermore, the use of multiple auxiliary chains for storing data across different application domains not only mitigates the risks associated with data expansion but also achieves micro-segmentation, thereby enhancing the efficiency of access control. Finally, empirical evidence demonstrates that, compared with the traditional methods, this paper’s scheme improves the encryption efficiency by 14%, reduces the data access latency by 18%, and significantly improves the throughput. This mechanism ensures data security while maintaining system efficiency in environments with large-scale data interactions.