Abstract: Molecular evolutionary researches is a field developed more fast in morden biological evolutionary researches,and has got great progress.At the same time,there are also some problems need to be solved.Up to now,according to the published researching articles on molecular evolution,we can see some conceptional confusion.For example,the examination had not been done all in the characters of biosystem,and difference between the molecular and biological evolution is confused in a certain degree,so it causes the mistakes in methodology which the mathematical methods treating linear system are used simply in treating nonlinear biosystem.So that the researched results of molecular administrative levels are extended simply and unconditionaly to nonlinear biological individual or popular level.Therefore it leads to some faults.We do write the article to stress the concept that biosystem is a system of nonlinear administrative level construction,and discuss the difference between molecular and biological evolution for the purpose of making the biologists concentrtion.We also investigate and review preliminary the problems that the structures of biomacromolecular one-,two- and tree-dimensions relating to molecular evolution in the paper,in order to explore the methodology of molecular evolutionary researches.The author considers that at the same time for doing the researches of molecular evolution,one must pay enough attention to the problems of administrative levels that exist between biomacromolecular one- and three- dimensions amd from the linear to the nonlinear.