To address the modeling fragmentation and predictive deviation caused by the conventional “single-mechanism, weakly coupled, additive response” approach in formation damage research, this study proposes an integrated modeling framework for multi-mechanism coupling throughout the entire drilling and completion process. Five dominant damage mechanisms are unified into a multi-physics formulation featuring a dual solid–liquid module architecture and a shared-state coupling mechanism. A structural-state integrated damage function (SSIDF) is introduced to establish a continuous mapping from microscopic mechanism evolution to macroscopic permeability degradation. A feedback network encompassing scaling, clay swelling, and water blocking is further developed, achieving bidirectional dynamic coupling among reaction kinetics, interfacial transport, and saturation fields, and representing one of the most systematic coupling schemes currently known. The model is solved via a space-time multi-scale optimization strategy, ensuring strong numerical stability and scalability. Field validation demonstrates a prediction accuracy of 98.6%, representing an improvement of over 8% compared to traditional additive models. The model is particularly applicable to unconventional reservoirs such as deepwater formations, where multi-mechanism damage evolves rapidly and conventional additive models fail to capture dynamic coupling behavior.