The real-time computation of a three-dimensional pipe network flow is crucial for both pipe design and operational maintenance. This study devises a novel reduced-order configuration approach that combines the advantages of the acceleration characteristics of the reduced-order model and the structural applicability of the configuration model. First, a configuration model is established by categorizing sub-pipes extracted from a pipe network into sets based on the sub-pipes' type. Subsequently, reduced-order configurations are realized by a reduced-order model established for each type of configuration, enabling real-time computation of individual sub-pipes. Thus, the concatenation of sub-pipes allows the computation of an entire pipe network. A complex boundary–deep learning–reduced-order configuration model and a complex boundary–deep learning–reduced-order configuration–multi-source data–reduced-order configuration model integrated with a local multi-physical–discrete empirical interpolation method and a multi-source data fusion model are devised. These models were employed for the real-time computation and prediction of a three-dimensional velocity field for 300 snapshots composed of one to four sub-pipes extrapolated from a dataset of 294 pipe network snapshots composed of one to three sub-pipes. The maximum relative errors for snapshots from the dataset were similar to the limit precision of the proper orthogonal decomposition, with more precise accuracy than the relevant studies, indicating the excellent performance of our reduced-order configuration approach.