The root system characteristics, such as root length, root surface area and root biomass in different soil depths were studied to assessed the correlation between root system characteristics and aboveground biomass, root-shoot ratio. This research was conducted on gentle slope, steep slope, middle bar and artificial bank slope of four typical site types on the aquatic-terrestrial ecotone of Lijiang watershed. The result showed that:(1) Within the same site type, the root biomass, aboveground biomass and root-shoot ratio of different main herbaceous plants were different significantly; Root length and root surface had some differences in different site type. On steep slope and artificial bank slope, there were significant differences between root length and surface area(p<0.05). On middle bar, the difference of root surface area was significant(p<0.05).(2) Polygonum hydropiper and Conyza canadensis grow best on the gentle slope. Steep slope was the most suitable site for Sida rhombifolia L. and Achyranthes bidentata Bl. The middle bar was the most appropriate area for Tatarian aster and Artemisia argyi. Artificial bank can provide the optimum environment for the growth of Humulus scandens Merr.