To address the frequent changes, dynamic evolution, and complex collaboration of BOM (Bill of Materials) under ETO (Engineer-to-Order) mode, this paper proposes a dual-layer BOM-based change control model. First, to enable model definition and change expression throughout the product lifecycle, a version control-based BOM model is defined by introducing material revision, material relationship links, and a multi-view mechanism, while also constructing a general BOM structure system. Then, to ensure traceability of product structural changes and cross-view consistency in the ETO mode, we design a dual-layer change traceability model. This model features vertical version chains and horizontal view collaboration traceability as its core components. Finally, an ETO-oriented BOM change operation model is constructed to standardize both in-view change operations and cross-view cooperative operations. This standardization enhances change control capability and lifecycle traceability efficiency of product structures in ETO manufacturing environments. The application of this model in a large equipment manufacturing enterprise shows that it significantly improves the change response efficiency and provides strong support for the digital transformation and supply chain collaboration of ETO enterprises.