Bearing fault diagnosis is critical for maintaining the reliability of health monitoring in electromechanical systems. However, traditional feature extraction methods often struggle to accurately capture fault information in complex environments. This paper proposes an adaptive tuning feature mode decomposition (ATFMD) method, based on the intrinsic signal characteristics, to effectively extract robust features. ATFMD dynamically adjusts to complex fault signals, providing more representative feature inputs and pruning redundant features induced by noise. Additionally, given the limitations of single-dimensional feature domains in fully revealing fault information, this study constructs feature topology graphs by mapping spatial phase and time–frequency characteristics, offering a comprehensive representation of fault information. To achieve complementary fusion of fault information within the feature topological graph, this paper proposes the synergy graph enhanced transformer (SGET). SGET optimizes the fusion process by reinforcing feature interactions through its synergy graph representation module. Additionally, a hierarchical cross-attention mechanism is employed to modulate attention distribution across feature dimensions, enhancing the sensitivity to critical features during fusion. Experimental validation was conducted on two distinct rotating machinery transmission systems. The results demonstrate that the proposed method maintains exceptional robustness and generalization, even in the presence of severe noise and complex fault conditions. Compared to the leading methods, including MS-DGCNs, CapsFormer, TFT, and ConvFormer, the proposed method achieves notable accuracy improvements of 8.13 %, 8.71 %, 11.94 %, and 6.25 %, respectively, under challenging conditions.