Human activity has a greater influence on plants than on any of the other components of the environment. We used material from cultivated and wild Coptis teeta populations in the Hengduan Mountains to test the null hypothesis that there is no effect of human activity on the biomass allocation of an herbaceous understory species in a forest ecosystem. At the plot level, an isometric relationship existed in most of the significant relationships. However, at the individual level, an allometric relationship existed in most of the log–log relationships. Human activity could significantly affect the slope of the linear relationship of leaf versus total biomass; and also the intercepts of the relationships of root biomass versus total biomass, plant height versus total biomass and reproductive versus vegetative biomass. At any given plant body size, wild C. teeta has higher biomass in the leaf and less in root than cultivated counterpart. But the trajectories of log rhizome biomass versus log total biomass were the same for both cultivated and wild individuals. Thus, we conclude that (1) the allometric trajectories change at different scales and (2) C. teeta‐based agroforestry system could ensure sustainable use of this medicinal plant because of the stable biomass allocation to the salable rhizome organs.