Computer-aided map overlay analysis is an efficient means of multi-element analysis. It nay be used in the synthetic qualitative and quantitative analysis of varied elements of environment and resources. It includes polygon overlay analysis and grid overlay analysis. The paper deals with the principle and method of polygon overlay analysis as well as the basic thoughto of its programming. Its application fields in the studies of natural resources are examined. A practical example is given to illustrate the method and course of using it. Computer-aided map overlay analysis may be applied to statistical calculation, classification, assessment of natural resources, etc. It is of practical significance to the studies of natural resources, especially agricultural land resources.