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This study investigates the tidal discharge division and phase difference at branches connected to a channel junction. The tidal discharge at three branches (eastern, western, and northern branches) was continuously collected using the fluvial acoustic tomography system (FATS). The discharge asymmetry index was used to quantify the flow division between two seaward branches (eastern and western branches). The cross-wavelet method was applied to calculate the phase difference between the tidal discharge and water level. The discharge asymmetry index shows that the inequality of flow division is obviously prominent during the spring tide duration, where the eastern branch has the capability to deliver greater amounts of subtidal discharge, approximately 55–63%, compared with the western branch. However, the equality of flow division between the eastern and western channels can be observed clearly during the neap tide period. The wavelet analysis shows that the phase difference at the western branch is higher than at the eastern branch, because the geometry of the western branch is more convergent than that of the eastern branch. Accordingly, the amplitude of the tidal wave at the western branch is more magnified compared with that at the eastern branch. Moreover, the phase difference at the northern branch is greater than at the two seaward branches, implying that the phase difference is slightly increased after passing through the junction into the northern branch.