Deep transfer learning (DTL) is a fundamental method in the field of Intelligent Fault Detection (IFD). It aims to mitigate the degradation of method performance that arises from the discrepancies in data distribution between training set (source domain) and testing set (target domain). Considering the fact that fault data collection is challenging and certain faults are scarce, DTL-based methods face the limitation of available observable data, which reduces the detection performance of the methods in the target domain. Furthermore, DTL-based methods lack comprehensive uncertainty analysis that is essential for building reliable IFD systems. To address the aforementioned problems, this paper proposes a novel DTL-based method known as Neural Processes-based deep transfer learning with graph convolution network (GTNP). Feature-based transfer strategy of GTNP bridges the data distribution discrepancies of source domain and target domain in high-dimensional space. Both the joint modeling based on global and local latent variables and sparse sampling strategy reduce the demand of observable data in the target domain. The multi-scale uncertainty analysis is obtained by using the distribution characteristics of global and local latent variables. Global analysis of uncertainty enables GTNP to provide quantitative values that reflect the complexity of methods and the difficulty of tasks. Local analysis of uncertainty allows GTNP to model uncertainty (confidence of the fault detection result) at each sample affected by noise and bias. The validation of the proposed method is conducted across 3 IFD tasks, consistently showing the superior detection performance of GTNP compared to the other DTL-based methods.