In industrial production engineering, machines cannot sustain faults for extended periods, resulting in limited fault data collection. This scarcity of data impedes the advancement of accurate fault diagnosis models, particularly in the context of small-sample, extremely imbalanced fault modeling, which poses a significant and challenging problem. In this paper, we introduce an innovative data augmentation approach for addressing the small-sample imbalanced problem: the balanced conditioning CNN (Convolutional Neural Networks)-Transformer architecture based Generative Adversarial Network (BCTGAN). Firstly, we employ a serial CNN and Transformer architecture as the foundation of the generator. Secondly, we introduce micro-enhancement and SMOTE (Synthetic Minority Oversampling Technique) enhancement of samples to facilitate model training. Micro-enhancement simply augments the sample size, while SMOTE enhancement enhances diversity. Together, these techniques balance the training process by introducing new loss function terms. Finally, outlier samples are mitigated through a designed multi-domain feature screening method. Despite the added time cost and computational complexity, results from three instances demonstrate that the proposed method holds superior diagnostic results with great potential compared to traditional and general GAN-based fault diagnosis methods. Our work provides theoretical and practical insights for modeling the field of small-sample blended disequilibrium fault diagnosis.