Changes of river morphology are closely related to discharge, transport capacity, and sediment supply. This study derives the equilibrium equation of sediment and defines two indexes, the sediments generation index IP and the sediments transportation and deposition index IR. Focusing on the impact of Typhoon Fanapi and Typhoon Megi on the Lan-Yang River watershed, this study investigates the control factors of the above two indexes, including topography, geology, rainfall, river morphology, landslide, etc. The results suggest that the sediments generated by Fanapi were transported to the middle segments of the Lan-Yang River. However, there are still areas with severe sediment accumulation, where treatments including dredging or earth working are necessary. Those areas need to be carefully handled since they are highly prone to becoming a secondary hazard due to typhoons or heavy rain.