Mixing in pipe junctions can play an important role in exciting force and distribution of flow in pipe network. This paper investigated the cross pipe junction and proposed an improved plan, Y-shaped pipe junction. The numerical study of a three-dimensional pipe junction was performed for calculation and improved understanding of flow feature in pipe. The filtered Navier–Stokes equations were used to perform the large-eddy simulation of the unsteady incompressible flow in pipe. From the analysis of these results, it clearly appears that the vortex strength and velocity non-uniformity of centerline, can be reduced by Y-shaped junction. The Y-shaped junction not only has better flow characteristic, but also reduces head loss and exciting force. The results of the three-dimensional improvement analysis of junction can be used in the design of pipe network for industry.