Real-time surface defect inspection plays an important role in the quality control of automated production. For the surface defect inspection, flowing data are a common data form in the automated pipeline production. Although flowing data provide rich information for surface defect inspection, there are still a lot of dynamic distribution challenges caused by the flowing data, such as the domain shift phenomenon and imbalanced training data. However, many existing industrial inspection solutions still use static strategies. To determine the dynamic distribution influence on the data flow domain, this article proposes a new deep ensemble learning method with domain fluctuation adaptation. Specifically, a new distribution discrepancy identifier based on estimation of the data set distribution and data characteristic is proposed. It utilizes advantages of both the deep convolutional neural network (CNN) and the shallow feature-based learning method to achieve higher robustness and fine-grained detection in streaming data scenes. In order to validate the proposed method, an inspection bench test system, as a part of a real industrial surface mount technology production line, is designed and fabricated. The proposed inference model is successfully applied to an embedded terminal with a hybrid and heterogeneous computing architecture. At last, the method is validated on the data collected from the manufacturer. The result suggests that the proposed method possesses a competitive mean average precision (mAP) rate with good adaptation and robustness in industrial streaming data scenes.