With Chinese medicine (CM) gaining popularity in recent years, researchers and clinicians have put in much interest and effort into the makings and effects of it, especially after the recent announcement of World Health Orgnitation’s incorporation of CM into mainstream medical compendium. Individual herb has complex properties, coming from its pharmacological properties and the Chinese medical principles of organ-directed, taste and dynamic orientational behaviours. The use of individual herb in CM is rare, where various herbs/ingredients are mostly found in a prescribed formula. To fully reveal the effects of CM is a great challenge. The complexity of various herbs in combined effect, the absorption and utility rate by the body, uniqueness of individual physique, sub-types of pathological behaviors and time-line progression of the healing process add on to the complication of understanding the full effect of CM. Various theories such as pathophysiology guidance, pharmacokinetic-pharmacodynamic compatibility method, and Global Systems Biology for Integrative Genomics, Proteomics and Metabolomics, which interactively provide a wider scope, more details, with the consideration of development timeline, may shed more light to revealing the full picture of the effects of compatibility prescription.