Abstract: The purpose of this study is to identify the types of allelopathic compounds in a hydroponic system and their effects on plants if they accumulate in hydroponic root system of plant for a long time. A new technology of separating and enriching root secretions from acuminata seedlings and wild Ophiorrhiza cantoniensis cultivated in GUANGZHOU had been established: silica gel were used as a filler of the solid phase extraction column to extract compounds from the hydroponic solution; then took the filler out and added in the top of the Silica gel column to separate the allelopathic compounds, After elution, the technology of GC-MS were used to analyze the constituents. By this technology, many allelopathic compounds in hydroponic root secretions of these two plants had been identified. 11 allelopathic compounds were found in root secretion of acuminata seedlings such as Ethane, 1,1,2,2-tetrachloroethane, N,N-Dimethylaniline, dibenzene-chromium and so on.12 allelopathic compounds were identified in root secretion of Ophiorrhiza cantoniensis such as Dibutyl phthalate, Dioctyl phthalate, dibenzene-chromium and so on. Isolation, enrichment and analysis of allelochemicals in root exudates of two plant species containing camptothecin laid the foundation for eliminating growth inhibitors containing in root secretion of acuminata seedlings, optimizing water culture system and realizing high efficient biosynthesis of camptothecin.