Data-driven intelligent fault diagnosis methods have emerged as powerful tools for monitoring and maintaining the operating conditions of mechanical equipment. However, in real-world engineering scenarios, mechanical equipment typically operates under normal conditions, resulting in limited and imbalanced (L&I) data. This situation gives rise to label bias and biased training. Meanwhile, the current multi-source information fault diagnosis research to date has tended to focus on fault identification rather than effective feature fusion strategies. To solve these issues, a novel end-to-end mechanical fault diagnosis framework under limited & imbalanced data using multi-source information fusion is proposed to model data-level and algorithm-level ideas in a unified deep network for achieving effective multi-source information fusion under the L&I working conditions. From a data-level perspective, a data preprocessing operation is first employed to capture time–frequency information simultaneously. Subsequently, multi-source time–frequency information is fed into feature extractors with information discriminators to construct local and information-invariant feature maps with different scales to eliminate multi-source information domain shift. Then, the multi-source feature vectors are modeled by a multi-source information transformer-based neural network to achieve effective multi-source information fusion through cross-attention mechanism. Next, the global max pooling and global average pooling layers are leveraged to obtain the more representative features. Finally, from an algorithm-level perspective, a dual-stream diagnosis predictor with a binary diagnosis predictor and a multi-class diagnosis predictor is designed to synthesize the diagnostic results through a reweighing activation mechanism for addressing the L&I problems. Extensive experiments on four different multi-source information datasets show the superiority and promising performance of our method compared to the state-of-the-art methods, as evidenced by indicators from various aspects.