The earthquake and its associated geomorphic processes destroy mountain vegetation and soil. The loose material may bring the risk of siltation and swamping after entering the lake. To investigate the current situation of lake siltation and swamping in Jiuzhaigou after the earthquake as well as the impact of the loose materials, this study selected four lakes in Jiuzhaigou scenic area with different siltation and swamping and then conducted the field surveys. The comprehensive evaluation method of swamping was adopted to evaluate the current situation utilizing vegetation indicators as the main principle and siltation promotion effect as the subsidiary principle. Meanwhile, the unmanned aerial vehicle was used to acquire the information of the surrounding environment as well as the damage degree of the lake and the impact of loose material from seismic damage on the siltation and swamping of Jiuzhaigou lakes were further discussed. The results show that:(1) The swamping development model of the four lakes all evolved from the shore to the center of the lake. (2) The spatial distribution characteristics of siltation and swamping degree of various lakes are different, and the degree of development from high to low is shown as follows:Lake Colorful has the highest swamping degree with the northwest side being in the late stage of swamping (index value[3, 4]). Lake Mirror ranks the second with part of it having a high level of swamping (index value[1.5, 3]). The next is Lake Rhino with only the inlet and outlet of the lake being in the early stage of swamping (index value[1.5, 2.5]). Last is the Lake Arrow Bamboo with an overall swamping degree being in the early stage (index value[0, 1.5]). (3) The large amount of loose material caused by seismic damage increases the siltation of the lakeshore and promotes the expansion of aquatic vegetation, which is the main reason for the development of siltation and swamping of Jiuzhaigou lakes. Managers in charge should focus on the development of swamping on small lakes, inlets, outlets, and disaster-stricken spots.