Hypertext and hypermedia technology is the most important development related to electronic publications including CTJ-ROM and Internet materials. With hypermedia technology the structure of a publication can be rearranged to accommodate an easier cognition of the idea and concept transferred by it by linking the concepts which are represented by different media forms into an integrated concept. Essentially multimedia electronic atlas is a kind of electronic publication, which has many common characters with ordinary CD-ROM publications, such as their multimedia functions. For the deeper exploration of electronic atlas the understanding of the internal and general structure of the new media structure is very important. The aim of this paper is to discuss the internal structure of multimedia electronic atlas as a whole by applying the methodology of linguistics. In section 1 the authors introduce some basic concepts of hypertext, hypermedia and multimedia electronic atlas. As the main character of electronic atlas distinct from other hypermedia product, map is the primary information type, which is as important as text, picture, sound and animation. In section 2, the linguistic mechanism of hypermedia structure is systematically described at the two levels of function and form. It is stated that hypermedia has two-level analogy with writing language. That is, hypermedia structure is a kind of enhanced information carrier, which is the same as writing language in function. As for the formal analogy, hypermedia Structure can also be divided into different language units with syntax and semantics defined on them. Linguistic methodology can be applied to the research of the new media. In section 3, the linguistic mechanism of multimedia electronic atlas, as an example of hypermedia structure, is described in more detailed way. Here node is discussed as the language unit. A syntax-oriented division of node into smaller language units in hypermedia structure is given and the chunking operation is defined upon the different types of units as the internal generation mechanism of node. The other operations special for hypermedia, combination and linkage are again defined within and between page(s) respectively. The operations constitute the main body of syntax and semantics mechanism of electronic atlas. In section 4,a case study is given by introducing an electronic atlas authoring system developed by the authors. The system has been designed following the guidelines described in this paper. The authors conclude that the exploration and understanding of internal structure of multimedia electronic atlas can be very helpful to the improvement of the design of an authoring software system as well as electronic atlas itself. Linguistic methodology provides us a very promising conceptual tool to explore and understand it. Syntax aspect can help us design better authoring software to meet the needs of appearance and framework of electronic atlas, while semantic aspect can help us design better contents of electronic atlas to convey information more efficiently.