The inaccurate prediction of vibrations in blade-disk structures leads to frequent occurrences of failures in rotating machinery, such as air-engines. Existing methods often empirically treat the contact parameters of interfaces as globally constant and rarely consider manufacturing and assembly deviations, resulting in a deviation of prediction models from reality. This work presents a model for complex assembly structures that includes non-uniform distributions of normal contact stiffness and tangential friction coefficients at rough interfaces, while also introducing experimentally measured geometric deviations to enhance alignment with real-world conditions. Taking fir-tree blade-disk structure as an example, the accuracy of the proposed method is comprehensively verified by four measurement experiments and one modal experiment. Subsequently, the combined influence of rough interfaces and three experimentally measured geometric deviations on the overall modal characteristics of blade-disk structure are investigated, and their influencing mechanisms are revealed. The results indicate that ignoring the interface roughness and geometric deviations may significantly affect the prediction accuracy of the modal characteristics. The proposed method has great potential in the field of predicting the modal characteristics for complex assembly structures and optimizing the design of their machining and assembly processes.