The motion laws of flow structure and sediment transport in right-angled conjunction area of main and branch channels are complicated which makes the corresponding further researches into predicaments. Through summarizing and analyzing those previous corresponding results on the natures of flow structure and sediment transport in the conjunctions, the division characteristics of flow structure and sediment transport had been generalized. Meanwhile the calculation method of local head loss had been preliminary studied. A new equation for calculating the local head loss coefficient associated with the depth ratio and the length of backwater had been presented. The equation was verified by the experimental flume data of Changjiang River Scientific Research Institute. The verified results indicate that the calculated values agree well with the experiment values where the conjunction ratio is small.