In this paper, based on analyzing the status quo and key problem of research on nature of Chinese materia medica, we propose the thinking of research on nature of Chinese materia medica in view of genetic relationship. Namely, according to the cue of documents arrangement and data excavation, in certern scope of genetic relationship, difinite the common pharmaco-effect of the same nature of drug, and analyze the chemical composition correlated the nature of drug, further more, reveal the related regularity of nature of Chinese materia medica-pharmaco-effect- chemical composition. Linking the nature of Chinese materia medica, pharmaco-effect and chemical composition will provide original thinking and view angle to break through the key problem of research on nature of Chinese materia medica.