Most of the compound fault diagnosis methods regard the compound fault as a new single fault type, ignoring the interaction of internal single faults, and the fault analysis is vague in granularity and poor in interpretation. An improved Transformer-based compound fault decoupling diagnosis method was proposed for industrial environments with very little compound fault data. The diagnosis process included pre-processing, feature extraction and fault decoupling. With introducing the decoder of the Transformer, the cross-attention mechanism enables each single fault label to adaptively in the extracted feature layer focus on the discriminative feature region corresponding to the fault feature and predicts the output probability to achieve compound fault decoupling. Compound fault tests were designed to verify the effectiveness of the method compared with the advanced algorithms. The results showed that the proposed method had high diagnostic accuracy with a small number of single fault training samples and a very small number of compound fault training samples. The compound fault diagnosis accuracy reached 88.29% when the training set contained only 5 compound fault samples. Thus the new method has a significant advantage over other methods.