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Abstract Adhesive bonding of composite materials has become increasingly crucial for advanced engineering applications, offering unique advantages for lightweight and high-performance designs. This study presents a novel framework, physics-informed failure mode proportion prediction (PIFMP) model, for predicting failure mode proportions in composite adhesive joints, addressing critical gaps in understanding mixed-mode failure behaviors. In contrast to conventional approaches that focus solely on force or stress prediction, this research integrates important parameters from multistage manufacturing processes (MMPs) and simulation data into a physics-informed machine learning (PIML) framework, enabling proactive failure prediction and design optimization. The proposed framework unifies data-driven machine learning models with features derived from finite element analysis (FEA), incorporating cohesive zone modeling (CZM) to capture the physical dynamics of adhesive behavior under lap shearing. By embedding FEA-based physics features into the machine learning process and leveraging a time-series transformer model to analyze the temporal progression of interfacial damage and separation, the framework ensures predictive accuracy and physics-informed consistency, enabling precise analysis of failure mechanisms. The empirical study validates the effectiveness and the reliability of the framework, demonstrating enhanced predictive performance through cross-validation. The work establishes a foundational approach for failure analysis and provides a robust basis for future advancements.