Managing versions of data for building information modeling (BIM) data is critical for design collaboration, especially with multiple disciplines involved where each team has specific data requirements and design procedures. However, existing version control approaches are still inefficient for two limitations: (1) lacking an efficient data structure for managing version dependencies among multi-disciplinary BIM models and (2) risking data manipulation due to a centralized versioning architecture that may lead to reworking, losing design traceability and raising disputes. Blockchain technology is an emerging and promising solution for version management as it provides a decentralized, immutable, and traceable database paradigm. Hence, this paper proposes a blockchain-aided solution for secure and efficient BIM versioning with three major innovations. Firstly, a two-layer container common data environment (TLCCDE) model integrating blockchain and Interplanetary File System (IPFS) is developed to illustrate an overall logic for BIM versioning in a distributed environment. Secondly, a smart contract swarm (SCS) is developed to automate versioning actions in the TLCCDE. Thirdly, a novel multi-branch structure (MBS) with efficient algorithms is designed to simultaneously manage version change continuity, issue attachment, and dependency compliance. The proposed TLCCDE model is evaluated and validated in design scenarios based on a real-world project. Results show that: (1) the TLCCDE model is workable in BIM versioning; (2) TLCCDE computing performance metrics, including SCS latency and throughput, as well as MBS latency and scalability, are all validated to be practical; and (3) the TLCCDE outperforms existing versioning approaches by augmenting dependency automation and versioning cybersecurity. •Proposes a two-layer container common data environment (TLCCDE) model for secure BIM versioning.•Develops a smart contract swarm (SCS) to automate version change activities in a blockchain.•Develops a multi-branch structure (MBS) for efficient management of BIM version branches.•Validates security performance of SCS and computational efficiency of MBS algorithm.•Results show the TLCCDE enables efficient and secure versioning and outperforms existing solutions.