The archive files of CERN (Chinese Ecosystem Research Network) stations should be encoded for effective management.This paper points out several rules for encoding the archive files: the object-oriented, the uniqueness, the simplicity and suitability, the reasonability, the expendablity and the normality.Based on the object-oriented rule which is the fundamental one, we think it essential to encode the archive files form the viewpoint of the structure and function of ecosystem.The paper puts forth the classification of lake ecosystem research area in the aspects of environment, the structure, material cycle and informatic transmission of ecosystem.A Three-level framework for coding is established and subsquently an 8-bit encoding method proposed: the first and second bits represent the code of CERN stationsj the third and fourth the code of certain field of ecosystem research;and the others the free code.